Re: [votca] LAMMPS Angle Potential in Degrees
2017-02-13 18:24 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>: > Hi Christoph, > > Thanks again for your quick message. > > It seems to run ok after the update. > > However, I think the forces are not correct in the LAMMPS table files. I > might be mistaken. > > I'm attaching the input files needed to generate the run with > (toVotca.tar.gz) > > csg-inverse --options settings.xml > > Below is a plot of what the Bond and Angle force from the generated table > files (table_b1.pot and table_a1.pot) after step001. I'm taking a simple > derivative as -deltaU/delta_r or -deltaU/delta_theta, and they don't seem > to match up with what VOTCA is outputting for the forces in the file. I > believe for the angle, that LAMMPS is expecting -dU/dtheta. > We had a discussion about LAMMPS' table format a while ago here: <https://groups.google.com/d/msg/votca/xGJnFSrFXYQ/Thg8kIyoYBoJ> and the code was written by Frank here: <https://groups.google.com/d/msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ> I think, for bonds the 4th column is -r*deltaU/delta_r, while for angle and dihedral it is just the negative derivative, but I guess the code was never really tested. Have a look at: < https://github.com/votca/csg/commit/6db1e9f22f4db0f0967e2ed525af31878cf73eaf > Let me know if it fixes it. Otherwise, send me a patch for table_to_tab.pl. Christoph > Consequently, the temperature blows up nearly immediately, and then you > see warnings in LAMMPS like "WARNING: 87 of 91 force values in table are > inconsistent with -dE/dr. Should only be flagged at inflection points > (../bond_table.cpp:380)". For some reason the angle potential is not > triggering this warning, but I believe it should because it also does not > appear to be consistent. (Note: checking the lammps source, it appears > this check is not in the angle table code, so that's probably the reason.) > > The energies and forces from the pair coefficients appear to be correct. > > Any ideas about what I might be doing wrong, or a potential fix? I'm also > not getting perfect agreement to the potential of mean force (e.g., > -kTln(Pr))for the step001 angle and bond potentials either, but this might > partially be due to the shifting you are doing. > > Thanks again for your help. > > Josh > > Bonds: > > > Angles: > > > > On Monday, February 13, 2017 at 6:11:08 PM UTC-5, Christoph Junghans wrote: > >> 2017-02-13 14:06 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>: >> > Thanks. I see now in step001. It does convert the table_a1.pot file >> as you >> > said. >> > >> > The issue seems to be that the LAMMPS potential file generated converts >> the >> > min/max from radians to degrees, but the 0.01 isn't >> converted, >> > so it tries to write out > 180 degrees in the LAMMPS file (18001 >> points) or >> > up to 18001*0.01*180/3.1415 = 10314.12 degrees. Is there a special way >> to >> > specify this step size after the unit conversion? >> Sorry, I just realized there is a bug the potential conversion for >> lammps. The conversion factor is applied twice. >> 3.1415*(180/3.1415)**2=10313.5. >> >> I fixed that now: >> <https://github.com/votca/csg/commit/cb92bcd6b84a60b05698b5e >> 409fc9d125959f03e> >> >> That said, the support for lammps as a simulation backend is still >> pretty rudimentary in VOTCA. >> >> Christoph >> >> > >> > Thanks for all your help with this. >> > >> > >> > Here is tail of the table_a1.pot LAMMPS file. >> > >> > 17989 1.03064e+04 7.9841910e-04 6.9526739e-04 >> > 17990 1.03069e+04 3.9962120e-04 6.9677605e-04 >> > 17991 1.03075e+04 0.000e+00 6.9814120e-04 >> > 17992 1.03081e+04 -4.0036230e-04 6.9936284e-04 >> > 17993 1.03087e+04 -8.0138340e-04 7.0044097e-04 >> > 17994 1.03092e+04 -1.2029811e-03 7.0137559e-04 >> > 17995 1.03098e+04 -1.6050732e-03 7.0216670e-04 >> > 17996 1.03104e+04 -2.0075775e-03 7.0281430e-04 >> > 17997 1.03109e+04 -2.4104117e-03 7.0331839e-04 >> > 17998 1.03115e+04 -2.8134936e-03 7.0367897e-04 >> > 17999 1.03121e+04 -3.2167410e-03 7.0389604e-04 >> > 18000 1.03127e+04 -3.6200716e-03 7.0396961e-04 >> > 18001 1.03132e+04 -4.0234033e-03 7.0389966e-04 >> > >> > >> > On Monday, February 13, 2017 at 3:59:10 PM UTC-5, Christoph Junghans >> wrote: >> >> >> >> 2017-02-13 13:43 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>: >> >> > Hi Christoph, >> >>
Re: [votca] Re: Pressure Correction LAMMPS
2017-02-16 10:20 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
> Hi Christoph,
>
> I think I have it basically working now, but I might be having a few issues.
> Here is what I did
>
> 1) I created a calc_pressure_lammps.sh file as you suggested. It is
> attached, but it is basically just calculating the average of a column of
> pressures I've outputted from LAMMPS using awk and assigning this to the
> p_new variable. I have hard coded the name of the lammps file (called
> lammps.pressure), as I wasn't sure how this could be read into the script.
Nice, it looks very good!
I would add an option to xml file in lammps block, e.g.
...
...
traj.dump
...
lammps.pressure
and then you can read its value inside the script using:
p_file="$(csg_get_property cg.inverse.lammps.pressure_file)"
If you want to allow a pressure file per-interaction add
to block inside the block
and use
p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)"
In addition, I would check if the pressure file exists before invoking awk:
[[ -f ${p_file} ]] || die "${0##*/}: pressure file '${p_file}" doesn't exist"
and check that awk actually ran correctly:
p_now=$(...) || die "${0##*/}: pressure averaging failed"
(Note "${0##*/}" is just the name of the script)
>
> 2)
> Added "pressure lammps calc_pressure_lammps.sh" in csg_table below "pressure
> gromacs calc_pressure_gromacs.sh"
>
> 3) Commented out in postupd_pressure.sh this line
>
> #[[ $sim_prog != gromacs ]] && die "${0##*/}: pressure correction for
> ${sim_prog} is not implemented yet!"
I would change it to that:
[[ $sim_prog != @(gromacs|lammps) ]] && die "${0##*/}: pressure
correction for ${sim_prog} is not implemented yet!"
so that it only works for lammps and gromacs
Can you do a pull request with these changes?
Details:
<https://github.com/votca/csg/wiki/BugFix#for-users-contribute-a-bug-fix>
>
> 4) It seems to be running and the pressure appears to be improving. I have
> 3 bead types for the hexane example, and 3 interactions, A-A, B-B, and A-B.
> VOTCA is only writing a A-A.pressure and a A-B.pressure file. It doesn't
> seem to be writing a B-B.pressure file, so I'm not sure if it is updating
> the B-B interaction??
That is a bit more tricky. I am guessing there is a typo in the xml
file, but I will look more in detail later.
I would look for the output and check:
- if the IBI update itself done for A-B
- if pressure is listed as a Post-update for the A-B interaction
- check inverse.log if calc_pressure_lammps.sh is called for A-B at all.
Christoph
>
> I am attaching the settings.xml file where I am calling for the pressure
> correction. Can you take a look to see if it is defined correctly there?
>
> In the *tar.gz I am attaching my current version of the ibi for LAMMPS with
> real units and pressure correction.
>
> Thanks again for all your help.
>
> Josh
>
>
> On Wednesday, February 15, 2017 at 11:05:47 AM UTC-5, Joshua Moore wrote:
>>
>> Hello,
>>
>> It appears the pressure correction for LAMMPS is not implemented.
>>
>> I saw this post by Frank
>>
>> https://groups.google.com/d/msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ
>>
>> It seems like in order to make it work, you would just have to feed in the
>> pressure from LAMMPS.
>>
>> What would be required for this?
>>
>> Could I have LAMMPS output an average pressure, and then this could be fed
>> into pressure_cor_simple.pl as my $p_now=$ARGV[0]; ??
>>
>> How does Gromacs do it? Does Gromacs calculate an average pressure and
>> that is fed in as $ARGV[0] into the perl script?
>>
>> Thanks.
>>
>> Josh
>
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Re: [votca] Re: Pressure Correction LAMMPS
2017-02-16 13:05 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
> Hi Christoph,
>
> Thanks again. I think I've implemented all your suggestions except for
>
> "If you want to allow a pressure file per-interaction add
> to block inside the block
> and use
> p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)" "
>
> I will have to think about that one. I think just a single pressure makes
> sense, no?
Multi-component pressure correction is bit tricky. You would need the
contribution from each individual interaction.
The standard version of Gromacs cannot calculated that and hence we
just use the total pressure.
You could also do a version where it fails back to total pressure,
something like:
p_file="$(csg_get_interaction_property --allow-empty
inverse.lammps.pressure_file)"
[[ -z ${p_file] ]] && p_file="$(csg_get_interaction_property
inverse.lammps.pressure_file)"
One more thing, please add documentation for new xml options to
share/xml/csg_defaults.xml.
>
> The other issue was a typo. Thanks for suggesting that. I had
> in twice, the second time, with nothing in it,
> so think it overrides the previous block. Seems to be updating now.
Good that you found it, I have seen that problem before!
Christoph
>
> I will do a pull request later today after a bit more testing, but I think
> it's ok now.
>
> Thanks.
>
> Josh
>
>
>
> On Thursday, February 16, 2017 at 1:46:29 PM UTC-5, Christoph Junghans
> wrote:
>>
>> 2017-02-16 10:20 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>:
>> > Hi Christoph,
>> >
>> > I think I have it basically working now, but I might be having a few
>> > issues.
>> > Here is what I did
>> >
>> > 1) I created a calc_pressure_lammps.sh file as you suggested. It is
>> > attached, but it is basically just calculating the average of a column
>> > of
>> > pressures I've outputted from LAMMPS using awk and assigning this to the
>> > p_new variable. I have hard coded the name of the lammps file (called
>> > lammps.pressure), as I wasn't sure how this could be read into the
>> > script.
>> Nice, it looks very good!
>>
>> I would add an option to xml file in lammps block, e.g.
>>
>> ...
>>
>>
>> ...
>> traj.dump
>> ...
>> lammps.pressure
>>
>>
>>
>> and then you can read its value inside the script using:
>> p_file="$(csg_get_property cg.inverse.lammps.pressure_file)"
>> If you want to allow a pressure file per-interaction add
>> to block inside the block
>> and use
>> p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)"
>>
>> In addition, I would check if the pressure file exists before invoking
>> awk:
>> [[ -f ${p_file} ]] || die "${0##*/}: pressure file '${p_file}" doesn't
>> exist"
>> and check that awk actually ran correctly:
>> p_now=$(...) || die "${0##*/}: pressure averaging failed"
>>
>> (Note "${0##*/}" is just the name of the script)
>> >
>> > 2)
>> > Added "pressure lammps calc_pressure_lammps.sh" in csg_table below
>> > "pressure
>> > gromacs calc_pressure_gromacs.sh"
>> >
>> > 3) Commented out in postupd_pressure.sh this line
>> >
>> > #[[ $sim_prog != gromacs ]] && die "${0##*/}: pressure correction for
>> > ${sim_prog} is not implemented yet!"
>> I would change it to that:
>> [[ $sim_prog != @(gromacs|lammps) ]] && die "${0##*/}: pressure
>> correction for ${sim_prog} is not implemented yet!"
>> so that it only works for lammps and gromacs
>>
>> Can you do a pull request with these changes?
>> Details:
>> <https://github.com/votca/csg/wiki/BugFix#for-users-contribute-a-bug-fix>
>>
>> >
>> > 4) It seems to be running and the pressure appears to be improving. I
>> > have
>> > 3 bead types for the hexane example, and 3 interactions, A-A, B-B, and
>> > A-B.
>> > VOTCA is only writing a A-A.pressure and a A-B.pressure file. It
>> > doesn't
>> > seem to be writing a B-B.pressure file, so I'm not sure if it is
>> > updating
>> > the B-B interaction??
>> That is a bit more tricky. I am guessing there is a typo in the xml
>> file, but I will look more in detail later.
>> I would look for the output and check:
>> - if the IBI update itself done for A-B
>> - if pressure is listed as a Post-update
Re: [votca] Re: Pressure Correction LAMMPS
2017-02-16 13:29 GMT-07:00 Sikandar Mashayak <symasha...@gmail.com>:
>
>
> On Thu, Feb 16, 2017 at 2:23 PM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> 2017-02-16 13:05 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
>> > Hi Christoph,
>> >
>> > Thanks again. I think I've implemented all your suggestions except for
>> >
>> > "If you want to allow a pressure file per-interaction add
>> > to block inside the block
>> > and use
>> > p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)" "
>> >
>> > I will have to think about that one. I think just a single pressure
>> > makes
>> > sense, no?
>> Multi-component pressure correction is bit tricky. You would need the
>> contribution from each individual interaction.
>> The standard version of Gromacs cannot calculated that and hence we
>> just use the total pressure.
>
>
> Won't this cause extra counting/corrections to the multiple interactions,
> i.e., multiple pair potentials will be modified to correct the same pressure
> resulting in over corrections and hence, error.
You can use individual scaling factors (e.g. 0.25,0.5, 0.25) to
correct for that statically.
>
> I think, either the pressure correction should be added to only one
> interaction for a given iteration or use partial pressures corresponding to
> each interaction to compute the pressure corrections.
I usually prefer the former approach, too, but it doesn't work very
well if one of the two species is underrepresented and hence you
correct for a pressure, which mostly comes from a different
interaction.
Christoph
>
> Best,
> Sikandar
>
>>
>> You could also do a version where it fails back to total pressure,
>> something like:
>> p_file="$(csg_get_interaction_property --allow-empty
>> inverse.lammps.pressure_file)"
>> [[ -z ${p_file] ]] && p_file="$(csg_get_interaction_property
>> inverse.lammps.pressure_file)"
>>
>> One more thing, please add documentation for new xml options to
>> share/xml/csg_defaults.xml.
>>
>> >
>> > The other issue was a typo. Thanks for suggesting that. I had
>> > in twice, the second time, with nothing in
>> > it,
>> > so think it overrides the previous block. Seems to be updating now.
>> Good that you found it, I have seen that problem before!
>>
>> Christoph
>> >
>> > I will do a pull request later today after a bit more testing, but I
>> > think
>> > it's ok now.
>> >
>> > Thanks.
>> >
>> > Josh
>> >
>> >
>> >
>> > On Thursday, February 16, 2017 at 1:46:29 PM UTC-5, Christoph Junghans
>> > wrote:
>> >>
>> >> 2017-02-16 10:20 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>:
>> >> > Hi Christoph,
>> >> >
>> >> > I think I have it basically working now, but I might be having a few
>> >> > issues.
>> >> > Here is what I did
>> >> >
>> >> > 1) I created a calc_pressure_lammps.sh file as you suggested. It is
>> >> > attached, but it is basically just calculating the average of a
>> >> > column
>> >> > of
>> >> > pressures I've outputted from LAMMPS using awk and assigning this to
>> >> > the
>> >> > p_new variable. I have hard coded the name of the lammps file
>> >> > (called
>> >> > lammps.pressure), as I wasn't sure how this could be read into the
>> >> > script.
>> >> Nice, it looks very good!
>> >>
>> >> I would add an option to xml file in lammps block, e.g.
>> >>
>> >> ...
>> >>
>> >>
>> >> ...
>> >> traj.dump
>> >> ...
>> >> lammps.pressure
>> >>
>> >>
>> >>
>> >> and then you can read its value inside the script using:
>> >> p_file="$(csg_get_property cg.inverse.lammps.pressure_file)"
>> >> If you want to allow a pressure file per-interaction add
>> >> to block inside the block
>> >> and use
>> >> p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)"
>> >>
>> >> In addition, I would check if the pressure file exists before invoking
>> >> awk:
>> >> [[ -f ${p_file} ]] || die "${0##*/}: pressure file '$
Re: [votca] Re: Pressure Correction LAMMPS
2017-02-16 13:51 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
> Good discussion. I understand the pressure correction a little better now.
>
> I was doing
>
> A-A
>
> 1 0 0
>
> B-B
>
> 0 1 0
>
> A-B
>
> 0 0 1
>
> And applying the total pressure to each interaction. So that would work
> with 3 interactions? If you had 4, could you do
>
> 0 0 0 1 ??
Yes!
>
> Or you are saying, you could update them all in the same step, but just
> apply a scaling factor so that the total of all scale factors is 1?
The other option is to do 1 for all interaction, meaning do
pressure correction every step.
And adjust the scaling factor (i.e. XXX) to something smaller.
Christoph
>
> Thanks.
>
> Josh
>
> On Thursday, February 16, 2017 at 3:43:43 PM UTC-5, Christoph Junghans
> wrote:
>>
>> 2017-02-16 13:29 GMT-07:00 Sikandar Mashayak <symas...@gmail.com>:
>> >
>> >
>> > On Thu, Feb 16, 2017 at 2:23 PM, Christoph Junghans <jung...@votca.org>
>> > wrote:
>> >>
>> >> 2017-02-16 13:05 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>:
>> >> > Hi Christoph,
>> >> >
>> >> > Thanks again. I think I've implemented all your suggestions except
>> >> > for
>> >> >
>> >> > "If you want to allow a pressure file per-interaction add
>> >> > to block inside the block
>> >> > and use
>> >> > p_file="$(csg_get_interaction_property inverse.lammps.pressure_file)"
>> >> > "
>> >> >
>> >> > I will have to think about that one. I think just a single pressure
>> >> > makes
>> >> > sense, no?
>> >> Multi-component pressure correction is bit tricky. You would need the
>> >> contribution from each individual interaction.
>> >> The standard version of Gromacs cannot calculated that and hence we
>> >> just use the total pressure.
>> >
>> >
>> > Won't this cause extra counting/corrections to the multiple
>> > interactions,
>> > i.e., multiple pair potentials will be modified to correct the same
>> > pressure
>> > resulting in over corrections and hence, error.
>> You can use individual scaling factors (e.g. 0.25,0.5, 0.25) to
>> correct for that statically.
>>
>> >
>> > I think, either the pressure correction should be added to only one
>> > interaction for a given iteration or use partial pressures corresponding
>> > to
>> > each interaction to compute the pressure corrections.
>> I usually prefer the former approach, too, but it doesn't work very
>> well if one of the two species is underrepresented and hence you
>> correct for a pressure, which mostly comes from a different
>> interaction.
>>
>> Christoph
>> >
>> > Best,
>> > Sikandar
>> >
>> >>
>> >> You could also do a version where it fails back to total pressure,
>> >> something like:
>> >> p_file="$(csg_get_interaction_property --allow-empty
>> >> inverse.lammps.pressure_file)"
>> >> [[ -z ${p_file] ]] && p_file="$(csg_get_interaction_property
>> >> inverse.lammps.pressure_file)"
>> >>
>> >> One more thing, please add documentation for new xml options to
>> >> share/xml/csg_defaults.xml.
>> >>
>> >> >
>> >> > The other issue was a typo. Thanks for suggesting that. I had
>> >> > in twice, the second time, with nothing
>> >> > in
>> >> > it,
>> >> > so think it overrides the previous block. Seems to be updating now.
>> >> Good that you found it, I have seen that problem before!
>> >>
>> >> Christoph
>> >> >
>> >> > I will do a pull request later today after a bit more testing, but I
>> >> > think
>> >> > it's ok now.
>> >> >
>> >> > Thanks.
>> >> >
>> >> > Josh
>> >> >
>> >> >
>> >> >
>> >> > On Thursday, February 16, 2017 at 1:46:29 PM UTC-5, Christoph
>> >> > Junghans
>> >> > wrote:
>> >> >>
>> >> >> 2017-02-16 10:20 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>:
>> >> >> > Hi Christoph,
>> >> >> >
>> >> >> > I think I have it basically working now, but I mi
Re: [votca] LAMMPS Angle Potential in Degrees
2017-02-14 17:58 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>: > > Hi Christoph, > > I am still testing, but it appears to be correct if you remove the $r[$i] > multiplying the force in table_to_tab.pl for bonds and angles. The unit > conversions seem to be correct after all. I haven't tested dihedrals yet > though. I learned LAMMPS can handle dihedrals with degrees or radians but > angles only with degrees in the table files but requires a term in the header. > > So change this line in table_to_tab.pl for bonds in the LAMMPS section > > printf(OUTFILE "%i %12.5e %15.7e > %15.7e\n",$i+1,$r[$i],$pot[$i],-$pot_deriv[$i]*$r[$i]); > > to this > > printf(OUTFILE "%i %12.5e %15.7e > %15.7e\n",$i+1,$r[$i],$pot[$i],-$pot_deriv[$i]); > > It looks like you might have changed it for angles last night already? You > can probably recombine bonds, angles, dihedrals, as this line is the same for > all of them, although haven't tested dihedrals yet. > > The LAMMPS manual also "Currently" says the force is in force units for the > bond tables. It may very well have been different before. > > http://lammps.sandia.gov/doc/bond_table.html > > Thanks. I am getting good agreement now to ibi for the hexane example with > LAMMPS for pair potentials, bonds, and angles, although still running it > longer. The temperature appears stable. I've run each iteration up to 250,000 > MD steps so far. I fixed the forces for bond now: <https://github.com/votca/csg/commit/567a37802a748bf3a73345f39fb02d1a5903aabe> Christoph > > Josh > > > > On Tue, Feb 14, 2017 at 12:44 AM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> >> >> 2017-02-13 18:24 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>: >>> >>> Hi Christoph, >>> >>> Thanks again for your quick message. >>> >>> It seems to run ok after the update. >>> >>> However, I think the forces are not correct in the LAMMPS table files. I >>> might be mistaken. >>> >>> I'm attaching the input files needed to generate the run with >>> (toVotca.tar.gz) >>> >>> csg-inverse --options settings.xml >>> >>> Below is a plot of what the Bond and Angle force from the generated table >>> files (table_b1.pot and table_a1.pot) after step001. I'm taking a simple >>> derivative as -deltaU/delta_r or -deltaU/delta_theta, and they don't seem >>> to match up with what VOTCA is outputting for the forces in the file. I >>> believe for the angle, that LAMMPS is expecting -dU/dtheta. >> >> We had a discussion about LAMMPS' table format a while ago here: >> <https://groups.google.com/d/msg/votca/xGJnFSrFXYQ/Thg8kIyoYBoJ> >> and the code was written by Frank here: >> <https://groups.google.com/d/msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ> >> >> I think, for bonds the 4th column is -r*deltaU/delta_r, while for angle and >> dihedral it is just the negative derivative, but I guess the code was never >> really tested. >> >> Have a look at: >> < >> https://github.com/votca/csg/commit/6db1e9f22f4db0f0967e2ed525af31878cf73eaf> >> Let me know if it fixes it. Otherwise, send me a patch for table_to_tab.pl. >> >> Christoph >> >>> >>> Consequently, the temperature blows up nearly immediately, and then you see >>> warnings in LAMMPS like "WARNING: 87 of 91 force values in table are >>> inconsistent with -dE/dr. Should only be flagged at inflection points >>> (../bond_table.cpp:380)". For some reason the angle potential is not >>> triggering this warning, but I believe it should because it also does not >>> appear to be consistent. (Note: checking the lammps source, it appears >>> this check is not in the angle table code, so that's probably the reason.) >>> >>> The energies and forces from the pair coefficients appear to be correct. >>> >>> Any ideas about what I might be doing wrong, or a potential fix? I'm also >>> not getting perfect agreement to the potential of mean force (e.g., >>> -kTln(Pr))for the step001 angle and bond potentials either, but this might >>> partially be due to the shifting you are doing. >>> >>> Thanks again for your help. >>> >>> Josh >>> >>> Bonds: >>> >>> >>> Angles: >>> >>> >>> >>> On Monday, February 13, 2017 at 6:11:08 PM UTC-5, Christoph Junghans wrote: >>>> >>>> 2017-02-13 14:06 GMT-07:00 J
Re: [votca] Pressure Correction LAMMPS
2017-02-15 9:05 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>: > Hello, > > It appears the pressure correction for LAMMPS is not implemented. > > I saw this post by Frank > > https://groups.google.com/d/msg/votca/Jxsdz6v9QKw/OUVfYan8CwAJ > > It seems like in order to make it work, you would just have to feed in the > pressure from LAMMPS. > > What would be required for this? You will need to write a script calc_pressure_lammps.sh and add it to csg_table as a new line: "pressure lammps calc_pressure_lammps.sh" Look at the calc_pressure_gromacs.sh for an example, but in short the new script should create a file (name given as the first argument) which contains just one line "Pressure=XXX" when XXX is a number or "nan". You could calculated the pressure from the trajectory or parse another file to read the pressure from. > > Could I have LAMMPS output an average pressure, and then this could be fed > into pressure_cor_simple.pl as my $p_now=$ARGV[0]; ?? Just have lammps output it to a file and then have calc_pressure_lammps.sh average it and write a VOTCA-type pressure file. > > How does Gromacs do it? Does Gromacs calculate an average pressure and that > is fed in as $ARGV[0] into the perl script? Gromacs uses g_energy to read the pressure out of the energy file and it also does the average. The script is called here: <https://github.com/votca/csg/blob/master/share/scripts/inverse/postupd_pressure.sh#L42> but that is already generic. (We had support for pressure correction with Espresso MD in an earlier version) So for LAMMPS support only one script is missing. Christoph > > Thanks. > > Josh > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] CMake error during build, and solution
Hi Robert,
thanks for reporting, I turned it into a issue of github:
https://github.com/votca/tools/issues/8
On a side note, mkl is only needed if you are planning to build
votca-ctp, votca-csg isn't really using it.
Christoph
2017-01-19 10:55 GMT-07:00 Robert Elder <rmel...@gmail.com>:
> Hi Users:
>
> I just wanted to share a Votca compilation problem and solution I
> encountered recently. When running the build.sh script, as described here
> (https://github.com/votca/csg/wiki/Installing#from-source), I encountered
> this error:
>
> [snip]
>
> cleaning tools
> buidling tools
> Scanning dependencies of target votca_tools_manpages
> [ 0%] Built target votca_tools_manpages
> Scanning dependencies of target intel
> Scanning dependencies of target gitversion
> Current git revision is 7ca4a6d
> [ 0%] Built target gitversion
> Scanning dependencies of target votca_tools
> [ 2%] Creating directories for 'intel'
> [ 4%] Performing download step (download, verify and extract) for 'intel'
> [ 7%] -- downloading...
>
> src='http://software.intel.com/sites/default/files/managed/76/8c/intel-mkl-and-boost-example.zip'
>
> dst='/p/home/elderr/src/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip'
> timeout='none'
> [ 9%] Building CXX object
> src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o
> CMake Error at intel-stamp/download-intel.cmake:9 (file):
> file DOWNLOAD HASH mismatch
>
> for file:
> [/p/home/elderr/src/votca/src/tools/intel/src/intel-mkl-and-boost-example.zip]
> expected hash: [b957ee63a2167ad21b650b47726cd55c]
> actual hash: [d41d8cd98f00b204e9800998ecf8427e]
>
>
>
> make[2]: *** [intel/src/intel-stamp/intel-download] Error 1
> make[1]: *** [CMakeFiles/intel.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs
>
> [snip]
>
> Basically CMake failed because the hashes on intel-mkl-and-boost-example.zip
> did not match -- the reason being that the downloaded
> intel-mkl-and-boost-example.zip was a zero byte file! I have no idea why;
> perhaps some obscure problem on our machine. I don't know CMake well enough,
> but it seems to be running with multiple threads -- maybe a race condition
> on download vs. hash? Just speculation.
>
> Anyway I solved this by downloading the 'src' file from
> http://software.intel.com manually and putting it in the required location
> ('dst'). Then I reran the build script, it picked up where it left off and
> completed without a problem.
>
> Hopefully that helps someone. Thanks for this great tool!
> -Robert Elder
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
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> Visit this group at https://groups.google.com/group/votca.
> For more options, visit https://groups.google.com/d/optout.
--
Christoph Junghans
Web: http://www.compphys.de
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[votca] votca 1.3.1 released
Dear all, Votca 1.3.1 was released. It will most likely be the last version of the Votca 1.3 series as we are working heavily on Votca 1.4. The 1.3.1 release contains some minor bug fixes, most importantly a fix in the histogram class of tools and an improvement for cmake's detection of libgromacs in csg. Cheers, Christoph -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] csg_inverse terminates without inverse.log
2017-02-28 15:08 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > Thank you for the help. It works now. My mistake was in my settings.xml ( I > had an extra in the file). However, I also faced another > problem. The problem now is that, suppose I have two beads namely A1 and B1. > I have given dis.tgt for A1-B1. It is still asking me B1-A1 tables too. Do I > need to have both interactions? A1-B1 and B1-A1 interactions mentioned? No, you just need one! See the propane example: https://github.com/votca/csg-tutorials/blob/master/propane/ibi/settings.xml it only has A-B. Christoph > > On Monday, February 27, 2017 at 3:39:09 PM UTC-6, Christoph Junghans wrote: >> >> 2017-02-27 13:35 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >> > Hi there, >> > I had obtained bonded tabulated potentials for our study molecule using >> > csg_boltzmann. Then using the tables of bonded potential, I am working >> > on >> > the non-bonded interaction using csg_inverse. For this, I have edited >> > the >> > settings.xml and grompp.mdp, topol.top of propane tutorial for our >> > system. I >> > compared my files with the propane systems files for ibi run. However, >> > when >> > I ran the csg_inverse --options settings.xml, it terminates >> > (prints"Terminated") without any error message or inverse.log. Could you >> > help me answering what could I have been missing? >> 1.) Does the original tutorial work? (If not it might be a computer >> system issue). >> 2.) Make sure your settings.xml is a valid xml, check that with >> $ xmlwf settings.xml >> 3.) Run csg_inverse in debug mode: >> $ csg_inverse --debug --options settings.xml >> >> Christoph >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] csg_inverse terminates without inverse.log
2017-02-27 13:35 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > Hi there, > I had obtained bonded tabulated potentials for our study molecule using > csg_boltzmann. Then using the tables of bonded potential, I am working on > the non-bonded interaction using csg_inverse. For this, I have edited the > settings.xml and grompp.mdp, topol.top of propane tutorial for our system. I > compared my files with the propane systems files for ibi run. However, when > I ran the csg_inverse --options settings.xml, it terminates > (prints"Terminated") without any error message or inverse.log. Could you > help me answering what could I have been missing? 1.) Does the original tutorial work? (If not it might be a computer system issue). 2.) Make sure your settings.xml is a valid xml, check that with $ xmlwf settings.xml 3.) Run csg_inverse in debug mode: $ csg_inverse --debug --options settings.xml Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: initial CG configuration
2016-08-31 14:51 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Christoph, > >It is zero at 180 degree. As you see in the figure (ABAanglehis.png - > supposed to be table_a1.xvg), value is zero at 180 degree. > > What I did, I removed the distribution below 1.5, then it is extrapolated. > Is this maybe the cause of failure of the run? > > Do I need to redo csg_call based on this whole distribution instead of only > 1.5~3.14? If it is zero at 180, you should make sure the potential goes to a high value there! Are you trying to do IBI on the bonded interaction, too? Or are they fixed? Christoph > > Thank you. > > Best regards, > Changwoon Jang > > > On Wed, Aug 31, 2016 at 4:16 PM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> 2016-08-31 12:24 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > Dear Christoph, >> > >> > I have tested IBI with angle potential from hexane tutorial. I >> > replace >> > hexane angle potential with table_a1.xvg in my system. In topol.top, I >> > used >> > all tabulated angle potentials (8) instead of harmonic angles (2). >> Are you trying to do IBI on the bonded interaction, too? Or are they >> fixed? >> >> > >> >Now, it smoothly works. I think that the A-B-A type angle potential >> > (table_a1.xvg) has a problem. >> > >> >As you said, what does that mean of "you might want to extrapolate >> > toward >> > 180 degree at bit steeper"? I would like to refine the potential of >> > table_a1.xvg because of the rest of potentials look fine at least IBI >> > running. >> Does the angle distribution have a non-zero value at 180 degree? >> >> Christoph >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > On Wed, Aug 31, 2016 at 1:30 PM, Christoph Junghans <jungh...@votca.org> >> > wrote: >> >> >> >> 2016-08-31 10:58 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> >> > Dear Christoph, >> >> > >> >> > When I change only harmonic angle from tabulated angle for "TDM" >> >> > molecule in topology file (topol.top) as follow, it smoothly now >> >> > works. >> >> > The >> >> > rest of bond, angle, dihedral still usethe tabulated (8) potentials. >> >> > >> >> >What does this mean? Is The tabulated angle potential derived for >> >> > TDM >> >> > molecule incorrect? >> >> I just means something isn't ok with that potential. >> >> Look at the angle potentials of the original VOTCA paper >> >> <http://dx.doi.org/10.1021/ct900369w> >> >> From the tables you sent yesterday, you might want to extrapolate >> >> toward 180 degree at bit steeper. >> >> >> >> If you are doing IBI, you don't have to use the Boltzmann inverted >> >> potential, you can always start from a harmonic potential as the >> >> initial guess. >> >> >> >> >> >> Christoph >> >> >> >> > >> >> > [ angles ] >> >> > 1 3 2 21 1.0 <--- originally 8 >> >> > 1 3 4 21 1.0 <--- originally 8 >> >> > 1 3 5 21 1.0 <--- originally 8 >> >> > 2 3 4 21 1.0 <--- originally 8 >> >> > 2 3 5 21 1.0 <--- originally 8 >> >> > 4 3 5 21 1.0 <--- originally 8 >> >> > >> >> > >> >> > Best regards, >> >> > Changwoon Jang >> >> > >> >> > >> >> > >> >> > On Wed, Aug 31, 2016 at 11:46 AM, Christoph Junghans >> >> > <jungh...@votca.org> >> >> > wrote: >> >> >> >> >> >> 2016-08-31 9:25 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> >> >> > Dear Christoph, >> >> >> > >> >> >> > IBI still fails few iteration later the angle is going and >> >> >> > coming >> >> >> > at >> >> >> > the >> >> >> > boundary. See the figures. I am not sure why GROMACS does not >> >> >> > consider >> >> >> > the >> >> >> > PBC effect. The 201-202-203 angle
Re: [votca] Re: initial CG configuration
2016-08-31 16:15 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Christoph, > > I re-extrapolated ABA angle (table_a1.xvg). The initial distribution > of ABA angle from BI is in Figure 1. After doing "csg_call --options > options.xml --ia-type angle --ia-name angle --sloppy-tables > convert_potential gromacs input output", in the lower angle, the slope is > going down in Figure 2. > > Why is this happening? Sometimes VOTCA's automatism fail. We use the last 3 valid point to add an average for the extrapolation: <https://github.com/votca/csg/blob/master/share/scripts/inverse/potential_extrapolate.sh#L39> And in your case, that doesn't make it steep enough! You will need to do some fine-tweaking by hand-editing the file. To repeat my questions for the third time: Are you trying to do IBI on the bonded interaction, too? Or are they fixed? Christoph > > Thank you. > > Best regards, > Changwoon Jang > > > > On Wed, Aug 31, 2016 at 5:21 PM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> 2016-08-31 14:51 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > Dear Christoph, >> > >> >It is zero at 180 degree. As you see in the figure (ABAanglehis.png - >> > supposed to be table_a1.xvg), value is zero at 180 degree. >> > >> > What I did, I removed the distribution below 1.5, then it is >> > extrapolated. >> > Is this maybe the cause of failure of the run? >> > >> > Do I need to redo csg_call based on this whole distribution instead of >> > only >> > 1.5~3.14? >> If it is zero at 180, you should make sure the potential goes to a >> high value there! >> >> Are you trying to do IBI on the bonded interaction, too? Or are they >> fixed? >> >> Christoph >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > On Wed, Aug 31, 2016 at 4:16 PM, Christoph Junghans <jungh...@votca.org> >> > wrote: >> >> >> >> 2016-08-31 12:24 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> >> > Dear Christoph, >> >> > >> >> > I have tested IBI with angle potential from hexane tutorial. I >> >> > replace >> >> > hexane angle potential with table_a1.xvg in my system. In topol.top, >> >> > I >> >> > used >> >> > all tabulated angle potentials (8) instead of harmonic angles (2). >> >> Are you trying to do IBI on the bonded interaction, too? Or are they >> >> fixed? >> >> >> >> > >> >> >Now, it smoothly works. I think that the A-B-A type angle >> >> > potential >> >> > (table_a1.xvg) has a problem. >> >> > >> >> >As you said, what does that mean of "you might want to extrapolate >> >> > toward >> >> > 180 degree at bit steeper"? I would like to refine the potential of >> >> > table_a1.xvg because of the rest of potentials look fine at least IBI >> >> > running. >> >> Does the angle distribution have a non-zero value at 180 degree? >> >> >> >> Christoph >> >> > >> >> > Thank you. >> >> > >> >> > Best regards, >> >> > Changwoon Jang >> >> > >> >> > On Wed, Aug 31, 2016 at 1:30 PM, Christoph Junghans >> >> > <jungh...@votca.org> >> >> > wrote: >> >> >> >> >> >> 2016-08-31 10:58 GMT-06:00 Chang Woon Jang >> >> >> <changwoonj...@gmail.com>: >> >> >> > Dear Christoph, >> >> >> > >> >> >> > When I change only harmonic angle from tabulated angle for >> >> >> > "TDM" >> >> >> > molecule in topology file (topol.top) as follow, it smoothly now >> >> >> > works. >> >> >> > The >> >> >> > rest of bond, angle, dihedral still usethe tabulated (8) >> >> >> > potentials. >> >> >> > >> >> >> > What does this mean? Is The tabulated angle potential derived >> >> >> > for >> >> >> > TDM >> >> >> > molecule incorrect? >> >> >> I just means something isn't ok with that potential. >> >> >> Look at the
Re: [votca] IBI
Dear Arpita, first of all, please don't reply to a mail thread related to a different issue that make it really hard to search on the mailing list later, just start a new one. Second, I assume, you have solved your original issue, so please post your solution, so that others can learn from it. All emails get archived here: <https://groups.google.com/forum/#!forum/votca> for users to search. Now back to your new question. 2016-09-04 3:20 GMT-06:00 Arpita Srivastava (P15CY006) <srivastav...@iitj.ac.in>: > Dear VOTCA users, > > I am trying to modify my non-bonded potentials so as to get a better RDF > plot. i wish to modify the non-bonded potentials between the head bead and > the end bead of my coarse-grained molecule. I used the attached .xml and the > .mdp file. I got following error while running the csg_inverse command: > subscript /opt/votca1/share/votca/scripts/inverse/RDF_to_POT.pl > Q0-C5.dist.tgt Q0-C5.pot.new.raw.JtH (from tags rdf pot) failed. That means something went wrong in the initial conversion of the potential when using Boltzmann inversion. Have a look at the end of inverse.log, look above the error message. Christoph > > Please guide me what I should do > > Thanking You, > > Sincerely > Arpita Srivastava > Research Scholar, > Dept. of Chemistry, > IIT-Jodhpur. > > On Wed, Aug 31, 2016 at 5:28 PM, ArS <srivastav...@iitj.ac.in> wrote: >> >> Dear VOTCA users, >> >> I am trying to make modifications in my non-bonded potentials using >> iterative Boltzmann method. I wish to modify the non-bonded potentials >> between the head bead and the end bead of my coarse-grained molecule. I >> created an xml file according to my need but while running the csg_inverse >> command, I am getting an error as: >> >> >> # ERROR: >> # critical: 'cp conf.gro >> /home/iitj-ananya/Desktop/new-cg-a1/a1-traj-AA/replicate-along-z/nb-corrections/step_000' >> failed # >> >> Please tell me how to fix this error. I am attaching my .xml also, have a >> look at it and let me know if it contains any mistake. >> >> Thank You >> ArS >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] how to convert dihedral potential from csg_boltzmann to gromacs potential
2016-08-29 14:47 GMT-06:00 Christoph Junghans <jungh...@votca.org>: > 2016-08-29 14:37 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> Dear Christoph, >> >> >> What I have used is the following command with the options.xml file. >> >> >> >> >> >> dihedral >> 0.285 >> 0.615 Btw, this seems to be wrong. Or do you only want to use the value from 0.285 to 0.615 to become part of the xvg table? VOTCA distinguishes between regions to sample (given by min and max) and regions to extrapolate (-pi to +pi for dihedrals), which are specified below. >> 0.001 >> >> >> >> 1e8 >> 3.14 >> 0.001 >> >> >> >> >> >> csg_call --options options.xml --ia-type bond --ia-name dihedral >> convert_potential gromacs table_d1.xvg full_table_d1.xvg > That command is wrong as you don't convert a bond. > For bonds, the minimum for the xvg table will always be set to 0. > >> >> >> >> >> This gives only from 0 to 3.14. When I used the following command, it gives >> error. >> >> csg_call --options options.xml --ia-type dihedral --ia-name dihedral >> convert_potential gromacs table_d1.xvg full_table_d1.xvg > convert_potential takes a VOTCA table (in rad) not a xvg table. > VOTCA table have 3 columns, angle(rad), potential(in simulation > units), flag (i/o/u) > The lines which have valid point should have an "i", but in case of > doubt you can just leave the 3rd column empty. > > Christoph >> >> >> Callstack: >> /home/chang/PACKAGE/votca/bin/csg_call - linenumber 199 >> do_external - linenumber 176 in >> /home/chang/PACKAGE/votca/share/votca/scripts/inverse/functions_common.sh >> >> /home/chang/PACKAGE/votca/share/votca/scripts/inverse/potential_to_gromacs.sh >> - linenumber 123 >> do_external - linenumber 22 (see 'csg_call --cat function >> do_external') >> die - linenumber 2 (see 'csg_call --cat function die') >> # >> # >> # >> # ERROR: >> # >> # do_external: subscript >> # >> # /home/chang/PACKAGE/votca/share/votca/scripts/inverse/table_linearop.pl >> --on-x table_d1.xvg table_d1.pot.scale.Jdqcv 57.2957795 0 # >> # (from tags table linearop) failed >> # >> # Details can be found above >> # >> # >> # >> ## >> >> >> On Mon, Aug 29, 2016 at 4:27 PM, Christoph Junghans <jungh...@votca.org> >> wrote: >>> >>> 2016-08-29 14:08 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >>> > Dear Votca Users, >>> > >>> > >>> > Dihedral potential obtained from is range -3.14 to 3.14. I would >>> > like to >>> > convert it to gromacs format using csg_call. How do I make options.xml >>> > file? >>> What is the csg_call command you are running? >>> Do you use the "--ia-type dihedral" option to specify you are >>> converting a dihedral? >>> >>> Christoph >>> > When I use the following xml file, it only produce from 0 to 3.14 not >>> > -3.14. >>> > >>> > >>> > >>> > >>> > bond >>> > 0.285 >>> > 0.615 >>> > 0.001 >>> > >>> > >>> > >>> > 1e8 >>> > 3.14 >>> > 0.001 >>> > >>> > >>> > >>> > >>> > Thank you. >>> > >>> > >>> > Best regards, >>> > Changwoon Jang, >>> > >>> > -- >>> > You received this message because you are subscribed to the Google >>> > Groups >>> > "votca" group. >>> > To unsubscribe from this group and stop receiving emails from it, send >>> > an >>> > email to votca+unsubscr...@googlegroups.com. >>> > To post to this group, send email to votca@googlegroups.com. >>> > Visit this group at https://groups.google.com/group/votca. >>> > For more options, visit https://groups.google.com/d/optout. >>> >>> >>> >>> -- >>> Christoph Junghans >>> Web: http://
Re: [votca] warning
2016-08-29 13:32 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Votca Users, > >I have four dihedral distributions directly from csg_boltzmann. However, > only one dihedral distribution gives waning sign during IBI run as follows. > > WARNING: For the 359 non-zero entries for table 0 in table_d1.xvg the forces > deviate on average 196% from minus the numerical derivative of the potential That means something went wrong in the table conversion! > > > > Then, the IBI fails with Fatal error: 1 of the 1720 bonded interactions > could not be calculated because some atoms involved moved further apart than > the multi-body cut-off distance (2.02391 nm) or the two-body cut-off > distance (2.02391 nm), see option -rdd, for pairs and tabulated bonds also > see option -ddcheck That is most likely due to the above warning. > > > I am not sure why only one dihedral gives this warning and prevent IBI run. > Do you have any comments on that? IBI for dihedral interactions is a bit tricky and not very well testing in VOTCA, so you will need to do a bit a debugging on your side. Christoph > > I have converted dihedral distribution radian to angle (only first column) > due to the ibi requirement just using unit convert x*180/3.14 (x is > radian). > > Thank you. > > Best regards, > Changwoon Jang, > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] warning
Hi,
thanks for sending the potentials.
Here is what I did:
$ ls table_d*.txt
table_d1.txt table_d2.txt table_d3.txt table_d4.txt
# These are the potentials out of csg_boltzmann
$ cat table_d.xml
dihedral
-3.141
3.141
0.001
1e8
0.001
$ for i in table_d*.txt; do csg_call --options table_d.xml --ia-type
dihedral --ia-name dihedral --sloppy-tables convert_potential gromacs
$i ${i%.txt}.xvg; done
This basically does:
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d1.txt table_d1.xvg
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d2.txt table_d2.xvg
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d3.txt table_d3.xvg
csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
--sloppy-tables convert_potential gromacs table_d4.txt table_d4.xvg
Please note you need the "--sloppy-tables" option as you want to
ignore the third column of table_d1.txt
Alternatively you could replace the 3rd column by "i":
$ awk '/^[^#]/{print $1,$2,"i"}' table_d1.txt > fixed_table_d1.txt
Then a I ran gromacs
$ gmx mdrun -tableb table_[abd]*.xvg -v
Please mind that this is gromacs 2016. which is why you need the
"-tableb" option. (Gromacs 5.0 was made obsolete a while back by its
developers.)
Seems to work for at least 10k steps.
Cheers,
Christoph
2016-08-29 20:52 GMT-06:00 Christoph Junghans <jungh...@votca.org>:
> 2016-08-29 15:19 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> Dear Christoph,
>>
>>Can I run ibi without dihedrals? Actually, I do not need dihedral
>> potentials even though CG molecules have dihedrals. Or, any suggestions for
>> debugging the dihedrals. Actually, the warning signs disappeared but I have
>> still the same Fatal error.
> Please send me the table and the xml off-list and I will have a look.
>
> And of course you can run IBI on a subset of the interactions, see
> <https://github.com/votca/csg-tutorials/tree/master/hexane/ibi>
> In this example only the non-bonded interactions are iterated.
>
> Christoph
>>
>> Thank you.
>>
>> Best regards,
>> Changwoon Jang
>>
>> On Mon, Aug 29, 2016 at 4:30 PM, Christoph Junghans <jungh...@votca.org>
>> wrote:
>>>
>>> 2016-08-29 13:32 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>>> > Dear Votca Users,
>>> >
>>> >I have four dihedral distributions directly from csg_boltzmann.
>>> > However,
>>> > only one dihedral distribution gives waning sign during IBI run as
>>> > follows.
>>> >
>>> > WARNING: For the 359 non-zero entries for table 0 in table_d1.xvg the
>>> > forces
>>> > deviate on average 196% from minus the numerical derivative of the
>>> > potential
>>> That means something went wrong in the table conversion!
>>> >
>>> >
>>> >
>>> > Then, the IBI fails with Fatal error: 1 of the 1720 bonded interactions
>>> > could not be calculated because some atoms involved moved further apart
>>> > than
>>> > the multi-body cut-off distance (2.02391 nm) or the two-body cut-off
>>> > distance (2.02391 nm), see option -rdd, for pairs and tabulated bonds
>>> > also
>>> > see option -ddcheck
>>> That is most likely due to the above warning.
>>> >
>>> >
>>> > I am not sure why only one dihedral gives this warning and prevent IBI
>>> > run.
>>> > Do you have any comments on that?
>>> IBI for dihedral interactions is a bit tricky and not very well
>>> testing in VOTCA, so you will need to do a bit a debugging on your
>>> side.
>>>
>>> Christoph
>>>
>>> >
>>> > I have converted dihedral distribution radian to angle (only first
>>> > column)
>>> > due to the ibi requirement just using unit convert x*180/3.14 (x is
>>> > radian).
>>> >
>>> > Thank you.
>>> >
>>> > Best regards,
>>> > Changwoon Jang,
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google
>>> > Groups
>>> > "votca" group.
>>> > To unsubscribe from this group and stop receiving emails from it, send
>>> > an
>>> > email to votca+unsubscr...@googlegroups.com.
>>> > To post to
Re: [votca] how to convert dihedral potential from csg_boltzmann to gromacs potential
2016-08-29 14:37 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Christoph, > > > What I have used is the following command with the options.xml file. > > > > > > dihedral > 0.285 > 0.615 > 0.001 > > > > 1e8 > 3.14 > 0.001 > > > > > > csg_call --options options.xml --ia-type bond --ia-name dihedral > convert_potential gromacs table_d1.xvg full_table_d1.xvg That command is wrong as you don't convert a bond. For bonds, the minimum for the xvg table will always be set to 0. > > > > > This gives only from 0 to 3.14. When I used the following command, it gives > error. > > csg_call --options options.xml --ia-type dihedral --ia-name dihedral > convert_potential gromacs table_d1.xvg full_table_d1.xvg convert_potential takes a VOTCA table (in rad) not a xvg table. VOTCA table have 3 columns, angle(rad), potential(in simulation units), flag (i/o/u) The lines which have valid point should have an "i", but in case of doubt you can just leave the 3rd column empty. Christoph > > > Callstack: > /home/chang/PACKAGE/votca/bin/csg_call - linenumber 199 > do_external - linenumber 176 in > /home/chang/PACKAGE/votca/share/votca/scripts/inverse/functions_common.sh > > /home/chang/PACKAGE/votca/share/votca/scripts/inverse/potential_to_gromacs.sh > - linenumber 123 > do_external - linenumber 22 (see 'csg_call --cat function > do_external') > die - linenumber 2 (see 'csg_call --cat function die') > # > # > # > # ERROR: > # > # do_external: subscript > # > # /home/chang/PACKAGE/votca/share/votca/scripts/inverse/table_linearop.pl > --on-x table_d1.xvg table_d1.pot.scale.Jdqcv 57.2957795 0 # > # (from tags table linearop) failed > # > # Details can be found above > # > # > # > ## > > > On Mon, Aug 29, 2016 at 4:27 PM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> 2016-08-29 14:08 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > Dear Votca Users, >> > >> > >> > Dihedral potential obtained from is range -3.14 to 3.14. I would >> > like to >> > convert it to gromacs format using csg_call. How do I make options.xml >> > file? >> What is the csg_call command you are running? >> Do you use the "--ia-type dihedral" option to specify you are >> converting a dihedral? >> >> Christoph >> > When I use the following xml file, it only produce from 0 to 3.14 not >> > -3.14. >> > >> > >> > >> > >> > bond >> > 0.285 >> > 0.615 >> > 0.001 >> > >> > >> > >> > 1e8 >> > 3.14 >> > 0.001 >> > >> > >> > >> > >> > Thank you. >> > >> > >> > Best regards, >> > Changwoon Jang, >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+unsubscr...@googlegroups.com. >> > To post to this group, send email to votca@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > > > -- > Best regards, > Changwoon Jang, > > Postdoctoral Research Fellow > Department of Chemical & Biological Engineering, Drexel University > 3141 Chestnut Street, Philadelphia, PA 19104 > > Voice: (662) 617-2267 > E-mail: cj...@drexel.edu > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] warning
2016-08-30 12:22 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
> Dear Christoph,
>
>Did you also change original bond and angle tables to gromacs format?
I only looked at the dihedral!
>
> If so, how do I determine the min and max values for bond and angle tables?
Basically you look at the distributions and find the well-sampled region.
For angle, usually 0 to pi works ok, but for the bond it is more hand tuning.
Christoph
>
>
>
> Thank you.
>
> Best regards,
> Changwoon Jang
>
> On Tue, Aug 30, 2016 at 2:04 PM, Christoph Junghans <jungh...@votca.org>
> wrote:
>>
>> Hi,
>>
>> thanks for sending the potentials.
>> Here is what I did:
>> $ ls table_d*.txt
>> table_d1.txt table_d2.txt table_d3.txt table_d4.txt
>> # These are the potentials out of csg_boltzmann
>> $ cat table_d.xml
>>
>>
>>
>> dihedral
>> -3.141
>> 3.141
>> 0.001
>>
>>
>>
>> 1e8
>> 0.001
>>
>>
>>
>> $ for i in table_d*.txt; do csg_call --options table_d.xml --ia-type
>> dihedral --ia-name dihedral --sloppy-tables convert_potential gromacs
>> $i ${i%.txt}.xvg; done
>> This basically does:
>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>> --sloppy-tables convert_potential gromacs table_d1.txt table_d1.xvg
>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>> --sloppy-tables convert_potential gromacs table_d2.txt table_d2.xvg
>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>> --sloppy-tables convert_potential gromacs table_d3.txt table_d3.xvg
>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>> --sloppy-tables convert_potential gromacs table_d4.txt table_d4.xvg
>> Please note you need the "--sloppy-tables" option as you want to
>> ignore the third column of table_d1.txt
>> Alternatively you could replace the 3rd column by "i":
>> $ awk '/^[^#]/{print $1,$2,"i"}' table_d1.txt > fixed_table_d1.txt
>> Then a I ran gromacs
>> $ gmx mdrun -tableb table_[abd]*.xvg -v
>> Please mind that this is gromacs 2016. which is why you need the
>> "-tableb" option. (Gromacs 5.0 was made obsolete a while back by its
>> developers.)
>>
>> Seems to work for at least 10k steps.
>>
>> Cheers,
>>
>> Christoph
>>
>>
>>
>> 2016-08-29 20:52 GMT-06:00 Christoph Junghans <jungh...@votca.org>:
>> > 2016-08-29 15:19 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> >> Dear Christoph,
>> >>
>> >>Can I run ibi without dihedrals? Actually, I do not need dihedral
>> >> potentials even though CG molecules have dihedrals. Or, any suggestions
>> >> for
>> >> debugging the dihedrals. Actually, the warning signs disappeared but I
>> >> have
>> >> still the same Fatal error.
>> > Please send me the table and the xml off-list and I will have a look.
>> >
>> > And of course you can run IBI on a subset of the interactions, see
>> > <https://github.com/votca/csg-tutorials/tree/master/hexane/ibi>
>> > In this example only the non-bonded interactions are iterated.
>> >
>> > Christoph
>> >>
>> >> Thank you.
>> >>
>> >> Best regards,
>> >> Changwoon Jang
>> >>
>> >> On Mon, Aug 29, 2016 at 4:30 PM, Christoph Junghans
>> >> <jungh...@votca.org>
>> >> wrote:
>> >>>
>> >>> 2016-08-29 13:32 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
>> >>> > Dear Votca Users,
>> >>> >
>> >>> >I have four dihedral distributions directly from csg_boltzmann.
>> >>> > However,
>> >>> > only one dihedral distribution gives waning sign during IBI run as
>> >>> > follows.
>> >>> >
>> >>> > WARNING: For the 359 non-zero entries for table 0 in table_d1.xvg
>> >>> > the
>> >>> > forces
>> >>> > deviate on average 196% from minus the numerical derivative of the
>> >>> > potential
>> >>> That means something went wrong in the table conversion!
>> >>> >
>> >>> >
>> >>> >
>> >>> > Then, the IBI fails with Fatal error: 1 of the 1720 bonded
>> >>> > interactions
>> &
Re: [votca] warning
2016-08-30 12:33 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>:
> Dear Christoph,
>
>It runs smoothly up to 12500 iterations. After that the error still exist
> as follows. Luckily, 10K iterations do not produce the error.
The below error means a bond got stretched more than 2.02391 nm, which
seems a bit unphysical.
You can look at your bond distributions if 2.02391 nm has a
probability greater than 0.
I guess, you will have to pick the min and max more carefully the xml
file for the bonds when using csg_call.
As rule of thumb min and max should lie on a downwards slopping, but
not quite 0 yet, part of the distribution.
After all the extrapolation csg_call does (see manual for details) the
potentials should look like a deformed U or W, you can check that by
look at the xvg output file.
Christoph
>
>
>
> DD step 12499 load imb.: force 5.6%
>
>Step Time Lambda
> 125006.250000.0
>
>Energies (kJ/mol)
> Tab. BondsTab. Angles Tab. Dih.LJ (SR) Coulomb (SR)
> 1.21732e+038.55168e+021.85141e+022.66780e+030.0e+00
> PotentialKinetic En. Total EnergyTemperature Pressure (bar)
> 4.92543e+033.80913e+038.73456e+033.13896e+021.21927e+03
>
>
> Not all bonded interactions have been properly assigned to the domain
> decomposition cells
>
> A list of missing interactions:
>Tab. Dih. of108 missing 1
>
> Molecule type 'JMT'
> the first 10 missing interactions, except for exclusions:
>Tab. Dih. atoms1234 global 927 928 929
> 930
>
> ---
> Program gmx, VERSION 5.0.8-dev-20151014-1f04b58
> Source code file:
> /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec_top.c, line:
> 394
>
> Fatal error:
> 1 of the 1720 bonded interactions could not be calculated because some atoms
> involved moved further apart than the multi-body cut-off distance (2.02391
> nm) or the two-body cut-off distance (2.02391 nm), see option -rdd, for
> pairs and tabulated bonds also see option -ddcheck
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> ---
>
> Best regards,
> Changwoon Jang
>
>
> On Tue, Aug 30, 2016 at 2:22 PM, Chang Woon Jang <changwoonj...@gmail.com>
> wrote:
>>
>> Dear Christoph,
>>
>>Did you also change original bond and angle tables to gromacs format?
>>
>> If so, how do I determine the min and max values for bond and angle
>> tables?
>>
>>
>>
>> Thank you.
>>
>> Best regards,
>> Changwoon Jang
>>
>> On Tue, Aug 30, 2016 at 2:04 PM, Christoph Junghans <jungh...@votca.org>
>> wrote:
>>>
>>> Hi,
>>>
>>> thanks for sending the potentials.
>>> Here is what I did:
>>> $ ls table_d*.txt
>>> table_d1.txt table_d2.txt table_d3.txt table_d4.txt
>>> # These are the potentials out of csg_boltzmann
>>> $ cat table_d.xml
>>>
>>>
>>>
>>> dihedral
>>> -3.141
>>> 3.141
>>> 0.001
>>>
>>>
>>>
>>> 1e8
>>> 0.001
>>>
>>>
>>>
>>> $ for i in table_d*.txt; do csg_call --options table_d.xml --ia-type
>>> dihedral --ia-name dihedral --sloppy-tables convert_potential gromacs
>>> $i ${i%.txt}.xvg; done
>>> This basically does:
>>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>>> --sloppy-tables convert_potential gromacs table_d1.txt table_d1.xvg
>>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>>> --sloppy-tables convert_potential gromacs table_d2.txt table_d2.xvg
>>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>>> --sloppy-tables convert_potential gromacs table_d3.txt table_d3.xvg
>>> csg_call --options table_d.xml --ia-type dihedral --ia-name dihedral
>>> --sloppy-tables convert_potential gromacs table_d4.txt table_d4.xvg
>>> Please note you need the "--sloppy-tables" option as you want to
>>> ignore the third column of table_d1.txt
>>> Alternatively you could replace the 3rd column by "i":
>>> $ awk '/^[^#]/{print $1,$2,"i"}' table_d1.txt > fixed_table_d1.txt
>>> Then a I ran gromacs
>>> $ gmx mdrun -tableb table_[abd]*.xvg -v
>>>
Re: [votca] warning
2016-08-30 13:18 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Christoph, > > I think that bond potentials seem to be good with U shape using > csg_call --options options.xml --ia-type bond --ia-name bond > convert_potential gromacs Yeah, the attached bond potentials actually look decent. I have another idea, see below... > > > The following potentials in figures are obtained from csg_call. I am not > sure of forces though. With all those potentials, now it does not run even > single iteration. > > > > Started mdrun on rank 0 Tue Aug 30 15:10:53 2016 >Step Time Lambda > 00.00.0 > > >Energies (kJ/mol) > Tab. BondsTab. Angles Tab. Dih.LJ (SR) Coulomb (SR) > 5.01406e+031.41421e+052.15701e+022.49642e+030.0e+00 > PotentialKinetic En. Total EnergyTemperature Pressure (bar) > 1.49147e+053.66788e+031.52815e+053.02256e+021.68470e+03 > > DD step 9 load imb.: force 6.7% > > > Not all bonded interactions have been properly assigned to the domain > decomposition cells > > A list of missing interactions: > Tab. Angles of856 missing 1 This could be a problem too. That means there is a missing interaction for one angle! Christoph > > Molecule type 'TDM' > the first 10 missing interactions, except for exclusions: > Tab. Angles atoms132 global 201 203 202 > > --- > Program gmx, VERSION 5.0.8-dev-20151014-1f04b58 > Source code file: > /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec_top.c, line: > 394 > > Fatal error: > 1 of the 1720 bonded interactions could not be calculated because some atoms > involved moved further apart than the multi-body cut-off distance (2.02391 > nm) or the two-body cut-off distance (2.02391 nm), see option -rdd, for > pairs and tabulated bonds also see option -ddcheck > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > --- > > Best regards, > Changwoon Jang > > > > On Tue, Aug 30, 2016 at 2:54 PM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> 2016-08-30 12:33 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > Dear Christoph, >> > >> >It runs smoothly up to 12500 iterations. After that the error still >> > exist >> > as follows. Luckily, 10K iterations do not produce the error. >> The below error means a bond got stretched more than 2.02391 nm, which >> seems a bit unphysical. >> You can look at your bond distributions if 2.02391 nm has a >> probability greater than 0. >> I guess, you will have to pick the min and max more carefully the xml >> file for the bonds when using csg_call. >> As rule of thumb min and max should lie on a downwards slopping, but >> not quite 0 yet, part of the distribution. >> After all the extrapolation csg_call does (see manual for details) the >> potentials should look like a deformed U or W, you can check that by >> look at the xvg output file. >> >> Christoph >> > >> > >> > >> > DD step 12499 load imb.: force 5.6% >> > >> >Step Time Lambda >> > 125006.250000.0 >> > >> >Energies (kJ/mol) >> > Tab. BondsTab. Angles Tab. Dih.LJ (SR) Coulomb >> > (SR) >> > 1.21732e+038.55168e+021.85141e+022.66780e+03 >> > 0.0e+00 >> > PotentialKinetic En. Total EnergyTemperature Pressure >> > (bar) >> > 4.92543e+033.80913e+038.73456e+033.13896e+02 >> > 1.21927e+03 >> > >> > >> > Not all bonded interactions have been properly assigned to the domain >> > decomposition cells >> > >> > A list of missing interactions: >> >Tab. Dih. of108 missing 1 >> > >> > Molecule type 'JMT' >> > the first 10 missing interactions, except for exclusions: >> >Tab. Dih. atoms1234 global 927 928 929 >> > 930 >> > >> > --- >> > Program gmx, VERSION 5.0.8-dev-20151014-1f04b58 >> > Source code file: >> > /home/chang/PACKAGE/votca/src/gromacs/src/gromacs/mdlib/domdec_top.c, >> > line: >&g
Re: [votca] warning
2016-08-29 15:19 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Christoph, > >Can I run ibi without dihedrals? Actually, I do not need dihedral > potentials even though CG molecules have dihedrals. Or, any suggestions for > debugging the dihedrals. Actually, the warning signs disappeared but I have > still the same Fatal error. Please send me the table and the xml off-list and I will have a look. And of course you can run IBI on a subset of the interactions, see <https://github.com/votca/csg-tutorials/tree/master/hexane/ibi> In this example only the non-bonded interactions are iterated. Christoph > > Thank you. > > Best regards, > Changwoon Jang > > On Mon, Aug 29, 2016 at 4:30 PM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> 2016-08-29 13:32 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > Dear Votca Users, >> > >> >I have four dihedral distributions directly from csg_boltzmann. >> > However, >> > only one dihedral distribution gives waning sign during IBI run as >> > follows. >> > >> > WARNING: For the 359 non-zero entries for table 0 in table_d1.xvg the >> > forces >> > deviate on average 196% from minus the numerical derivative of the >> > potential >> That means something went wrong in the table conversion! >> > >> > >> > >> > Then, the IBI fails with Fatal error: 1 of the 1720 bonded interactions >> > could not be calculated because some atoms involved moved further apart >> > than >> > the multi-body cut-off distance (2.02391 nm) or the two-body cut-off >> > distance (2.02391 nm), see option -rdd, for pairs and tabulated bonds >> > also >> > see option -ddcheck >> That is most likely due to the above warning. >> > >> > >> > I am not sure why only one dihedral gives this warning and prevent IBI >> > run. >> > Do you have any comments on that? >> IBI for dihedral interactions is a bit tricky and not very well >> testing in VOTCA, so you will need to do a bit a debugging on your >> side. >> >> Christoph >> >> > >> > I have converted dihedral distribution radian to angle (only first >> > column) >> > due to the ibi requirement just using unit convert x*180/3.14 (x is >> > radian). >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang, >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+unsubscr...@googlegroups.com. >> > To post to this group, send email to votca@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > > > -- > Best regards, > Changwoon Jang, > > Postdoctoral Research Fellow > Department of Chemical & Biological Engineering, Drexel University > 3141 Chestnut Street, Philadelphia, PA 19104 > > Voice: (662) 617-2267 > E-mail: cj...@drexel.edu > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] force constant in tabulated bond, angle, and dihedral
2016-08-30 18:48 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Votca Users, > > > I would like to know how to determine force constants for topol.top > from all tutorials. All the force constants k set 1.0. What is the criteria > for selecting the force constants? The potentials / forces in the xvg files made by VOTCA already have the right scales and hence we set the scale to 1.0 These constants are useful sometimes, imagine a case where the potentials, were iterated at T_1 and you wanted to run a simulation at T_2 and hence you have to scale all of them with (k_b*T_2)/(k_b*T1). > > Since the force constants are already listed in tabulated table in third > column, can you just set 1.0? Yes, just set them to 1.0. Christoph > > Thank you. > > Best regards, > Changwoon Jang, > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: initial CG configuration
2016-08-31 8:43 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Votca Users, > >I have missed the figures. Figure 1 is initial configuration. Figure 2 is > the final iteration (1000 iteration) right before the ibi fails. > > Thank you. > > Best regards, > Changwoon Jang > > > On Wed, Aug 31, 2016 at 10:35 AM, Chang Woon Jang <changwoonj...@gmail.com> > wrote: >> >> Dear Votca Users, >> >> I have a question about creating initial configuration of the system. >> >> 1. Full atomistic simulation I have run full atomistic >> simulations of polymer system with OPLS-AA force field. Then, it (low >> density system) was equilibrated with NVT and NPT simulation for 50 ns. >> Thus, the box under PBC is shrinked from 10nm to about 5nm. >> >> 2. Then, I used the final configuration (confout.gro) in order to map >> the atomistic system into Coarse-grained system. >> >> I used this CG system for IBI in order to get non-bonded potentials. >> However, when I run IBI, I think that some of angle are blowing up and the >> ibi run finally fail in the beginning. I checked CG trajectory. An angle >> seem to be blowing up as shown in figure. >> >>I think this is ok if the system is under PBC. But the error message >> keeps indicate this angle has a problem. You might want to run $ gmx trjconv -f conf_in.gro -o conf_out.gro -pbc mol to make molecule whole. Christoph >> >> >>Therefore, I am asking for how you create the initial CG system all >> beads are inside box but not at the boundary. >> >> Thank you. >> >> >> >> Not all bonded interactions have been properly assigned to the domain >> decomposition cells >> >> A list of missing interactions: >> Tab. Angles of856 missing 1 >> >> Molecule type 'TDM' >> the first 10 missing interactions, except for exclusions: >> Tab. Angles atoms132 global 201 203 202 >> >> >> ** >> >> Best regards, >> Changwoon Jang, >> > > > > -- > Best regards, > Changwoon Jang, > > Postdoctoral Research Fellow > Department of Chemical & Biological Engineering, Drexel University > 3141 Chestnut Street, Philadelphia, PA 19104 > > Voice: (662) 617-2267 > E-mail: cj...@drexel.edu > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: initial CG configuration
2016-08-31 9:25 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Christoph, > > IBI still fails few iteration later the angle is going and coming at the > boundary. See the figures. I am not sure why GROMACS does not consider the > PBC effect. The 201-202-203 angle looks like over 180 degree. Do you have > any suggestion? Well, not really. I guess it is time to debug your topology! I would start with using some harmonic interactions for all angles (with approximately the right mean and width) and replace them one by one to see, which one make the simulation crash. Christoph > > Thank you. > > Best regards, > Changwoon Jang > > On Wed, Aug 31, 2016 at 11:05 AM, Christoph Junghans <jungh...@votca.org> > wrote: >> >> 2016-08-31 8:43 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: >> > Dear Votca Users, >> > >> >I have missed the figures. Figure 1 is initial configuration. Figure >> > 2 is >> > the final iteration (1000 iteration) right before the ibi fails. >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > On Wed, Aug 31, 2016 at 10:35 AM, Chang Woon Jang >> > <changwoonj...@gmail.com> >> > wrote: >> >> >> >> Dear Votca Users, >> >> >> >> I have a question about creating initial configuration of the >> >> system. >> >> >> >> 1. Full atomistic simulation I have run full atomistic >> >> simulations of polymer system with OPLS-AA force field. Then, it (low >> >> density system) was equilibrated with NVT and NPT simulation for 50 ns. >> >> Thus, the box under PBC is shrinked from 10nm to about 5nm. >> >> >> >> 2. Then, I used the final configuration (confout.gro) in order to >> >> map >> >> the atomistic system into Coarse-grained system. >> >> >> >> I used this CG system for IBI in order to get non-bonded >> >> potentials. >> >> However, when I run IBI, I think that some of angle are blowing up and >> >> the >> >> ibi run finally fail in the beginning. I checked CG trajectory. An >> >> angle >> >> seem to be blowing up as shown in figure. >> >> >> >>I think this is ok if the system is under PBC. But the error message >> >> keeps indicate this angle has a problem. >> You might want to run >> $ gmx trjconv -f conf_in.gro -o conf_out.gro -pbc mol >> to make molecule whole. >> >> Christoph >> >> >> >> >> >>Therefore, I am asking for how you create the initial CG system all >> >> beads are inside box but not at the boundary. >> >> >> >> Thank you. >> >> >> >> >> >> >> >> >> >> Not all bonded interactions have been properly assigned to the domain >> >> decomposition cells >> >> >> >> A list of missing interactions: >> >> Tab. Angles of856 missing 1 >> >> >> >> Molecule type 'TDM' >> >> the first 10 missing interactions, except for exclusions: >> >> Tab. Angles atoms132 global 201 203 202 >> >> >> >> >> >> >> >> ** >> >> >> >> Best regards, >> >> Changwoon Jang, >> >> >> > >> > >> > >> > -- >> > Best regards, >> > Changwoon Jang, >> > >> > Postdoctoral Research Fellow >> > Department of Chemical & Biological Engineering, Drexel University >> > 3141 Chestnut Street, Philadelphia, PA 19104 >> > >> > Voice: (662) 617-2267 >> > E-mail: cj...@drexel.edu >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+unsubscr...@googlegroups.com. >> > To post to this group, send email to votca@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >
Re: [votca] Iterative boltzmann
2016-08-31 8:35 GMT-06:00 ArS <srivastav...@iitj.ac.in>: > Hi, > I included the configuration file to my working directory and to the xml > file as well, still the same error appears. Like Chandan said, something goes wrong when copying conf.gro, please refer to the more verbose error message at the end of inverse.log. There are two main errors, 1.) there is no "conf.gro" in the main directory, 2.) there is no space left on the drive. Christoph > > > On Wednesday, August 31, 2016 at 7:27:35 PM UTC+5:30, Chandan Choudhury > wrote: >> >> The error indicates that conf.gro is missing. >> >> On Wed, Aug 31, 2016 at 7:21 AM, <srivas...@iitj.ac.in> wrote: >>> >>> Dear VOTCA users, >>> I am performing iterative Boltzmann method to modify non-bonded >>> interactions between a head bead and the end bead of my coarse-grained >>> molecule. I have prepared an .xml file according to the but while running >>> the csg_inverse command, I am getting the error note as: >>> >>> ERROR: >>> # critical: 'cp conf.gro >>> /home/iitj-ananya/Desktop/new-cg-a1/a1-traj-AA/replicate-along-z/nb-corrections/step_000' >>> failed >>> >>> Can you please tell me where I am making mistake. I am also attaching my >>> .xml file. Please have a look at it and let me know if it has any mistake. >>> >>> Thank You. >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send an >>> email to votca+un...@googlegroups.com. >>> To post to this group, send email to vo...@googlegroups.com. >>> Visit this group at https://groups.google.com/group/votca. >>> For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> -- >> >> Chandan Kumar Choudhury >> Post Doctoral Fellow >> Clemson University >> South Carolina >> USA >> >> "All work and no play makes Jack a dull boy...” > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Angle distributions
2016-09-09 5:39 GMT-06:00 ArS <srivastav...@iitj.ac.in>: > Dear VOTCA users, > > I am coarse graining a surfactant molecule. I am deriving the bonded > potentials using Boltzmann inversion. First I got the distributions of > bonds and angles due to mapping of atomistic model to a coarse-grained > model, and from those distributions, bonded potentials were derived. > Then those potentials were used during the simulation. The non-bonded > potentials are obtained using the MARTINI force-field. After the 20 ns NPT > run of the coarse-grained system, I again checked for the distributions of > bonds and angles. While comparing the distributions due to AA-model and the > CG-model, the bond distributions match well but the angle distributions do > not. Specially for the head bead, the angle distribution is very different. > > This is how I generated the angle distributions by mapping AA model to CG > model: > > cat boltzmann_btm_analysis_angle_shape | csg_boltzmann --top > ../../../npt.tpr --trj ../../../npt-180ns.xtc --cg ../btm.xml --map-ignore > "STE;Cl;SOL" > > The "boltzmann_btm_analysis_angle_shape" is written as: > > hist angle.dist.ib *:angle1:* > tab set T 283 > tab set scale angle1 > tab angle.pot *:angle1:* > q > > After a run 0f 20 ns, the angle distribution of the coarse-grained model > is generated as: > cat boltzmann_shape | csg_boltzmann --top ../table.tpr --trj ../table.xtc > --cg map_btm.xml --map-ignore "STE;CL-;W" > > The boltzmann_shape is written as: > hist bond.without_shift_btm1.ib *bond1:* > hist bond.without_shift_btm2.ib *bond2:* > hist bond.without_shift_btm3.ib *bond3:* > hist bond.without_shift_btm4.ib *bond4:* > hist bond.without_shift_btm5.ib *bond5:* > hist angle.without_shift_btm1.ib *angle1:* > hist angle.without_shift_btm2.ib *angle2:* > > hist angle.without_shift_btm3.ib *angle3:* > hist angle.without_shift_btm4.ib *angle4:* > q > > While generating the tables for bonded and anglular potentials, I used > csg_resample command, in the --grid option, I used step of 0.002 (example > : --grid 0.00:0.002:3.142). Similarly, while exporting the tables using > csg_call --options, in the table.xml file, table_bins value is 0.002. > If I change the step and the table_bins values, can I get a better angle > potential so that the angle distribution of CG model matches with that of > the AA model? > I am afraid no, changing the bins sizes does very little to the potential and hence the distribution. Making the bins size smaller might help to resolve some peaks better, but it won't help with the shoulders of the distribution. > If there is any other way to modify the coarse-grained distribution, > please suggest me. > Use a different coarse-graining technique, e.g. force matching. > How can I shift the angle distributions? > What do you mean by shifting? Christoph -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: Segmentation fault (whilst using csg_fmatch)
Hi Rom, could please give version 1.3.1 and the latest development version a try, too? Christoph 2016-09-13 7:13 GMT-06:00 Rom <romnikthi...@gmail.com>: > Thanks Christoph! > > I have attached the xml file that I used (it is a very large system, and I > tried many min/max/block values), and the output error from my terminal I > have copied into a text file (csg_fmatch_error). > I used the exact same votca version I used before, and I also used > votca/1.2.4 on a different system and got the same segmentation fault. I > also used a variety of gromacs version (4.5.5, 4.6.7 etc). > > Rom > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: Segmentation fault (whilst using csg_fmatch)
2016-09-13 11:51 GMT-06:00 Rom <romnikthi...@gmail.com>: > > Sure, I will try to install it and see if it gets rid of the error! > Which version of gromacs is best compatible with Votca/1.2.4? Im just > confused why it works for one system, but not for the current system I am > trying to run? Wait, is the segfault in gromacs? Can you try to read the same topology and trajectory with a different VOTCA program (e.g. csg_map) and see if that segfaults, too? Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Angle distributions
2016-09-12 4:00 GMT-06:00 ArS <srivastav...@iitj.ac.in>: > I meant that is there any method to modify the tabulated angle potentials, > which are generated by inversion Boltzmann distribution? I think that my > angle potentials are wrong and hence the angular distribution due to the AA > simulation and those obtained after the coarse-grained simulation are > mismatched. > Well, if simple Boltzmann inversion doesn't work you might need to do iterative Boltzmann inversion. Another reason, why the distributions are off could be that you are mixing Boltzmann-inverted potentials with the MARTINI force-field. Mixing structure-based and free-energy-based potential gives unpredictable results. To check you could study a single molecule in vacuum and compare your bonded interactions. Christoph > > On Friday, September 9, 2016 at 8:26:07 PM UTC+5:30, Christoph Junghans > wrote: >> >> >> >> 2016-09-09 5:39 GMT-06:00 ArS <srivas...@iitj.ac.in>: >> >>> Dear VOTCA users, >>> >>> I am coarse graining a surfactant molecule. I am deriving the bonded >>> potentials using Boltzmann inversion. First I got the distributions of >>> bonds and angles due to mapping of atomistic model to a coarse-grained >>> model, and from those distributions, bonded potentials were derived. >>> Then those potentials were used during the simulation. The non-bonded >>> potentials are obtained using the MARTINI force-field. After the 20 ns NPT >>> run of the coarse-grained system, I again checked for the distributions of >>> bonds and angles. While comparing the distributions due to AA-model and the >>> CG-model, the bond distributions match well but the angle distributions do >>> not. Specially for the head bead, the angle distribution is very different. >>> >>> This is how I generated the angle distributions by mapping AA model to >>> CG model: >>> >>> cat boltzmann_btm_analysis_angle_shape | csg_boltzmann --top >>> ../../../npt.tpr --trj ../../../npt-180ns.xtc --cg ../btm.xml --map-ignore >>> "STE;Cl;SOL" >>> >>> The "boltzmann_btm_analysis_angle_shape" is written as: >>> >>> hist angle.dist.ib *:angle1:* >>> tab set T 283 >>> tab set scale angle1 >>> tab angle.pot *:angle1:* >>> q >>> >>> After a run 0f 20 ns, the angle distribution of the coarse-grained model >>> is generated as: >>> cat boltzmann_shape | csg_boltzmann --top ../table.tpr --trj >>> ../table.xtc --cg map_btm.xml --map-ignore "STE;CL-;W" >>> >>> The boltzmann_shape is written as: >>> hist bond.without_shift_btm1.ib *bond1:* >>> hist bond.without_shift_btm2.ib *bond2:* >>> hist bond.without_shift_btm3.ib *bond3:* >>> hist bond.without_shift_btm4.ib *bond4:* >>> hist bond.without_shift_btm5.ib *bond5:* >>> hist angle.without_shift_btm1.ib *angle1:* >>> hist angle.without_shift_btm2.ib *angle2:* >>> >>> hist angle.without_shift_btm3.ib *angle3:* >>> hist angle.without_shift_btm4.ib *angle4:* >>> q >>> >>> While generating the tables for bonded and anglular potentials, I used >>> csg_resample command, in the --grid option, I used step of 0.002 (example >>> : --grid 0.00:0.002:3.142). Similarly, while exporting the tables using >>> csg_call --options, in the table.xml file, table_bins value is 0.002. >>> If I change the step and the table_bins values, can I get a better angle >>> potential so that the angle distribution of CG model matches with that of >>> the AA model? >>> >> I am afraid no, changing the bins sizes does very little to the potential >> and hence the distribution. Making the bins size smaller might help to >> resolve some peaks better, but it won't help with the shoulders of the >> distribution. >> >> >>> If there is any other way to modify the coarse-grained distribution, >>> please suggest me. >>> >> Use a different coarse-graining technique, e.g. force matching. >> >> >>> How can I shift the angle distributions? >>> >> What do you mean by shifting? >> >> Christoph >> >> -- >>> You received this message because you are subscribed to the Google >>> Groups "votca" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to votca+un...@googlegroups.com. >>> To post to this group, send email to vo...@googlegroups.com. >>> Visit this group at https://groups.goog
Re: [votca] Installing VOTCA in OS X 10.11.6
gt; 120.1.0) > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version > 1226.10.1) > > And then I got stuck. > > How should I proceed? Can you check that /usr/local/fftw/lib/libfftw3.dylib actually exists? The error > make[1]: *** No rule to make target `/usr/local/fftw/lib/libfftw3.dylib' seems to indicate that cmake cannot read libfftw3.dylib! Christoph > Best regards. > Nancy > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Kirkwood–Buff Integrals for Finite Volumes
2016-10-05 1:29 GMT-06:00 Vitalie Botan <vitalie.bo...@gmail.com>: > Does it have any parameters to play with, like integral cutoff, fudge factor > etc.? Or in the current version it is all fixed to the values mentioned in > the paper? No, the beauty is that C-IBI is parameter-free. However, you still have the same options as IBI is having, e.g. update order and scaling factor. Christoph > > --Vitalie > > On Tuesday, October 4, 2016 at 5:19:42 PM UTC+2, Christoph Junghans wrote: >> >> >> See Fig. 8 of http://dx.doi.org/10.1063/1.4947253 for an xml sniplet. >> We are currently working on a tutorial and a manual update for >> inclusion in VOTCA 1.4 >> >> Christoph >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] installing Votca
2016-10-04 12:50 GMT-06:00 Devon Dillon <devondillon...@gmail.com>: > How do i fix this and How can i include missing files like this so it can be > easily addressed in the future? How did you resolve the boost issue? And you only need kmc if ultimately want to install ctp and if that is the case the question is for the votca-ctp mailing list! Christoph > > > On Tuesday, October 4, 2016 at 1:49:47 PM UTC-5, Devon Dillon wrote: >> >> I installed CSG successfully, however kmc now presents an issue >> >> In file included from >> /Users/Dillon/ProgramBuilds/VOTCA/src/kmc/src/libkmc/kmccalculatorfactory.cc:21: >> >> >> /Users/Dillon/ProgramBuilds/VOTCA/src/kmc/src/libkmc/calculators/kmcmultiple.h:38:10: >> fatal error: 'tr1/unordered_map' file not found >> >> #include >> >> ^ >> >> 1 error generated. >> >> make[2]: *** >> [src/libkmc/CMakeFiles/votca_kmc.dir/kmccalculatorfactory.cc.o] Error 1 >> >> make[2]: *** Waiting for unfinished jobs >> >> make[1]: *** [src/libkmc/CMakeFiles/votca_kmc.dir/all] Error 2 >> >> make: *** [all] Error 2 >> >> >> >> On Tuesday, October 4, 2016 at 12:18:57 PM UTC-5, Devon Dillon wrote: >>> >>> i cannot seem to get this resolved... any tips if it is not finding the >>> boost libraries? would i have to reinstall them since i installed cmake3.6.2 >>> >>> -- The following REQUIRED packages have not been found: >>> >>> >>> * Boost (required version >= 1.39.0) >>> >>> >>> -- Configuring incomplete, errors occurred! >>> >>> >>> On Tuesday, October 4, 2016 at 10:06:25 AM UTC-5, Christoph Junghans >>> wrote: >>>> >>>> 2016-10-04 8:37 GMT-06:00 Devon Dillon <devondi...@gmail.com>: >>>> > will this reduce the functionality of my votca program? >>>> No, you will just have no manpages! >>>> >>>> Christoph >>>> > >>>> > >>>> > On Tuesday, October 4, 2016 at 9:11:15 AM UTC-5, Christoph Junghans >>>> > wrote: >>>> >> >>>> >> 2016-10-04 7:00 GMT-06:00 Devon Dillon <devondi...@gmail.com>: >>>> >> > I'm having issues with installing csg. Can someone please point me >>>> >> > in >>>> >> > the >>>> >> > right direction? >>>> >> > >>>> >> > Scanning dependencies of target csg_fmatch_manpage >>>> >> > >>>> >> > [ 85%] Generating csg_fmatch.man >>>> >> > >>>> >> > dyld: Library not loaded: libvotca_tools.4.dylib >>>> >> > >>>> >> > Referenced from: >>>> >> > /Users/Dillon/ProgramBuilds/VOTCA/src/csg/src/tools/./csg_fmatch >>>> >> > >>>> >> > Reason: image not found >>>> >> > >>>> >> > /bin/sh: line 1: 65933 Trace/BPT trap: 5 ./csg_fmatch --help >>>> >> > > >>>> >> > csg_fmatch.help >>>> >> > >>>> >> > make[2]: *** [src/tools/csg_fmatch.man] Error 133 >>>> >> > >>>> >> > make[1]: *** [src/tools/CMakeFiles/csg_fmatch_manpage.dir/all] >>>> >> > Error 2 >>>> >> > >>>> >> > make[1]: *** Waiting for unfinished jobs >>>> >> > >>>> >> > [ 86%] Linking CXX executable template_serial >>>> >> > >>>> >> > [ 86%] Built target template_serial >>>> >> > >>>> >> > [ 88%] Linking CXX executable template_threaded >>>> >> > >>>> >> > [ 88%] Built target template_threaded >>>> >> > >>>> >> > make: *** [all] Error 2 >>>> >> > >>>> >> > what do i do to get this library to load? >>>> >> Try to build it without manpages (option -DBUILD_MANPAGES=OFF). >>>> >> >>>> >> Christoph >>>> >> > >>>> >> > -- >>>> >> > You received this message because you are subscribed to the Google >>>> >> > Groups >>>> >> > "votca" group. >>>> >> > To unsubscribe from this group and stop receiving emails from it, >>>> >> > se
Re: [votca] installing Votca
2016-10-04 7:00 GMT-06:00 Devon Dillon <devondillon...@gmail.com>: > I'm having issues with installing csg. Can someone please point me in the > right direction? > > Scanning dependencies of target csg_fmatch_manpage > > [ 85%] Generating csg_fmatch.man > > dyld: Library not loaded: libvotca_tools.4.dylib > > Referenced from: > /Users/Dillon/ProgramBuilds/VOTCA/src/csg/src/tools/./csg_fmatch > > Reason: image not found > > /bin/sh: line 1: 65933 Trace/BPT trap: 5 ./csg_fmatch --help > > csg_fmatch.help > > make[2]: *** [src/tools/csg_fmatch.man] Error 133 > > make[1]: *** [src/tools/CMakeFiles/csg_fmatch_manpage.dir/all] Error 2 > > make[1]: *** Waiting for unfinished jobs > > [ 86%] Linking CXX executable template_serial > > [ 86%] Built target template_serial > > [ 88%] Linking CXX executable template_threaded > > [ 88%] Built target template_threaded > > make: *** [all] Error 2 > > what do i do to get this library to load? Try to build it without manpages (option -DBUILD_MANPAGES=OFF). Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Installing VOTCA in OS X 10.11.6
Am 06.10.2016 11:32 schrieb "nancyfor" <nancy...@gmail.com>: > > Dear Christoph, > > For this, > >> sed: -: No such file or directory > >Can you track back where this error is coming from? > > I got the following while debugging > . > . > . > ++ get_version /Users/nancyfor/src/votca/src/./build.sh > ++ sed -ne 's/^#version[[:space:]]*\([^[:space:]]*\)[[:space:]]*-- .*$/\1/p' /Users/nancyfor/src/votca/src/./build.sh > ++ sed -n '$p' > + old_version=2.1.0 > + '[' -q = -q ']' > ++ get_webversion -q > ++ local version > ++ [[ -q = \-\q ]] > +++ wget -qO- https://raw.githubusercontent.com/votca/buildutil/master/build.sh > +++ get_version > +++ sed -ne 's/^#version[[:space:]]*\([^[:space:]]*\)[[:space:]]*-- .*$/\1/p' - > +++ sed -n '$p' > sed: -: No such file or directory I see, it must be here! > ++ version= > ++ echo '' > . > . > . > > >Can you check that /usr/local/fftw/lib/libfftw3.dylib actually exists? > In fact it does not exist, only static .a libraries are there. So I re-installed fftw using > > brew install fftw > > and got the dynamic ones. > > I tried to run it again, and got further, now it complains about my prefix, which i wanted to be src/votca, but it complains it needs a preceding "/", so used /src/votca/ which of course need root privileges to write > > this is the error message > > Install the project... > -- Install configuration: "Release" > CMake Error at src/libtools/cmake_install.cmake:31 (file): > file cannot create directory: /src/votca/lib. Maybe need administrative > privileges. > Call Stack (most recent call first): > src/cmake_install.cmake:32 (include) > cmake_install.cmake:32 (include) > > How do I keep my prefix=src/votca? I do no find the error here. You could use e.g. $HOME/votca Christoph > > Thanks for your help, > Nancy > > > > > > > > On Wednesday, 5 October 2016 18:06:07 UTC+2, Christoph Junghans wrote: >> >> 2016-10-05 7:40 GMT-06:00 nancyfor <nanc...@gmail.com>: >> > Hello, >> > >> > I am trying to install votca following the installation instructions here: >> > >> > https://github.com/votca/csg/wiki/CompilingOSX >> > >> > I have installed the dependencies, using the following versions >> > gsl-2-2 >> > fftw-3.3.4 >> > boost_1_62_0 >> > cmake 3.6.2 >> > >> > and tried to build it using >> > >> > ./build.sh --prefix $prefix -DWITH_FFTW=ON -DWITH_GSL=ON >> > -DGSL_INCLUDE_DIR=/usr/local/gsl/include >> > -DGSL_LIBRARY=/usr/local/gsl/lib/libgsl.dylib >> > -DCBLAS_LIBRARY=/usr/local/gsl/lib/libgslcblas.dylib >> > -DFFTW3_INCLUDE_DIR=/usr/local/fftw/include >> > -DFFTW3_LIBRARY=/usr/local/fftw/lib/libfftw3.dylib tools csg >> > >> > I got the following message >> > >> > sed: -: No such file or directory >> Can you track back where this error is coming from? >> >> > prefix has to be a global path (should start with a '/') >> > >> > I include the --debug option obtaining the following. >> > >> > . >> > . >> > . >> > + [[ 2.1.0 < '' ]] >> > + return 1 >> > + [[ 2 -eq 0 ]] >> > + [[ -z src/votca ]] >> > + [[ src/votca = *WHERE/TO/INSTALL/VOTCA* ]] >> > + [[ src/votca = /* ]] >> > + die 'prefix has to be a global path (should start with a '\''/'\'')' >> > + [[ -n prefix has to be a global path (should start with a '/') ]] >> > + cecho RED 'prefix has to be a global path (should start with a '\''/'\'')' >> > + local 'colors=BLUE CYAN CYANN GREEN RED PURP' >> > + [[ -z RED ]] >> > + [[ -z prefix has to be a global path (should start with a '/') ]] >> > + is_in RED 'BLUE CYAN CYANN GREEN RED PURP' >> > + [[ -z RED ]] >> > + [[ -z BLUE CYAN CYANN GREEN RED PURP ]] >> > + [[ BLUE CYAN CYANN GREEN RED PURP = *\ \R\E\D\ * ]] >> > + echo -n '' >> > + echo -e 'prefix has to be a global path (should start with a '\''/'\'')' >> > prefix has to be a global path (should start with a '/') >> > >> > By changing my prefix from src/votca to /src/votca I overcame this (but I am >> > not sure of where is going to be installed) and obtain the following message >> > >> > Could not find fftw_plan_r2r_1d in /usr/local/fftw/lib/libfftw3.dylib, take >> > a look at the error message in >> > .../votca/src/tools/CMakeFiles/CMakeError.log >> > >> > which shows >> > >> > Determining if the
Re: [votca] installing Votca
2016-10-04 8:37 GMT-06:00 Devon Dillon <devondillon...@gmail.com>: > will this reduce the functionality of my votca program? No, you will just have no manpages! Christoph > > > On Tuesday, October 4, 2016 at 9:11:15 AM UTC-5, Christoph Junghans wrote: >> >> 2016-10-04 7:00 GMT-06:00 Devon Dillon <devondi...@gmail.com>: >> > I'm having issues with installing csg. Can someone please point me in >> > the >> > right direction? >> > >> > Scanning dependencies of target csg_fmatch_manpage >> > >> > [ 85%] Generating csg_fmatch.man >> > >> > dyld: Library not loaded: libvotca_tools.4.dylib >> > >> > Referenced from: >> > /Users/Dillon/ProgramBuilds/VOTCA/src/csg/src/tools/./csg_fmatch >> > >> > Reason: image not found >> > >> > /bin/sh: line 1: 65933 Trace/BPT trap: 5 ./csg_fmatch --help > >> > csg_fmatch.help >> > >> > make[2]: *** [src/tools/csg_fmatch.man] Error 133 >> > >> > make[1]: *** [src/tools/CMakeFiles/csg_fmatch_manpage.dir/all] Error 2 >> > >> > make[1]: *** Waiting for unfinished jobs >> > >> > [ 86%] Linking CXX executable template_serial >> > >> > [ 86%] Built target template_serial >> > >> > [ 88%] Linking CXX executable template_threaded >> > >> > [ 88%] Built target template_threaded >> > >> > make: *** [all] Error 2 >> > >> > what do i do to get this library to load? >> Try to build it without manpages (option -DBUILD_MANPAGES=OFF). >> >> Christoph >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Kirkwood–Buff Integrals for Finite Volumes
2016-10-04 3:54 GMT-06:00 Vitalie Botan <vitalie.bo...@gmail.com>: > Hi Christoph, > > thanks for the reply, I am definitely going to try it the next days and will > let you know if it helps or makes any sense at all to implement. BTW, if you > already mentioned C-IBI (also announced in 1.4 release), do I need any > special commands/tags in the settings.xml for this method? Do you plan to > release also a new tutorial/example for it? See Fig. 8 of http://dx.doi.org/10.1063/1.4947253 for an xml sniplet. We are currently working on a tutorial and a manual update for inclusion in VOTCA 1.4 Christoph > > Regards, > --Vitaliy > >> >> It is not hard, I guess - you basically have to multiple the g(r)with >> h(x) from Eq. 7 before line 69 in >> >> <https://github.com/votca/csg/blob/master/share/scripts/inverse/postupd_cibi_correction.sh#L69> >> I would implement that in a similar fashion as >> >> <https://github.com/votca/csg/blob/master/share/scripts/inverse/table_switch_border.pl> >> which put a cos function over a table. >> >> Christoph >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] installing Votca
2016-10-04 8:49 GMT-06:00 Devon Dillon <devondillon...@gmail.com>: > Thank you very much! i have run into this error before but did not know how > to go about correcting it. Where do i need to insert the path to my boost > libraries? I know i have them downloaded because i can see them in a finder > window. You are too cutting edge! This is bug in cmake-3.6.0 and cmake-3.6.1, which don't support boost-1.61 and boost-1.62 It has been fixed in cmake-3.6.2: https://gitlab.kitware.com/cmake/cmake/commit/a997cac8323dc1764e092b8691857dd9af70956e Christoph > > -- Found Git: /usr/local/bin/git (found version "2.10.0") > > CMake Warning at > /ProgramBuilds/CMake.app/Contents/share/cmake-3.6/Modules/FindBoost.cmake:743 > (message): > > Imported targets not available for Boost version 106200 > > Call Stack (most recent call first): > > > /ProgramBuilds/CMake.app/Contents/share/cmake-3.6/Modules/FindBoost.cmake:842 > (_Boost_COMPONENT_DEPENDENCIES) > > > /ProgramBuilds/CMake.app/Contents/share/cmake-3.6/Modules/FindBoost.cmake:1395 > (_Boost_MISSING_DEPENDENCIES) > > CMakeLists.txt:48 (find_package) > > > > CMake Warning at > /ProgramBuilds/CMake.app/Contents/share/cmake-3.6/Modules/FindBoost.cmake:743 > (message): > > Imported targets not available for Boost version 106200 > > Call Stack (most recent call first): > > > /ProgramBuilds/CMake.app/Contents/share/cmake-3.6/Modules/FindBoost.cmake:842 > (_Boost_COMPONENT_DEPENDENCIES) > > > /ProgramBuilds/CMake.app/Contents/share/cmake-3.6/Modules/FindBoost.cmake:1395 > (_Boost_MISSING_DEPENDENCIES) > > CMakeLists.txt:48 (find_package) > > > > CMake Error at > /ProgramBuilds/CMake.app/Contents/share/cmake-3.6/Modules/FindBoost.cmake:1753 > (message): > > Unable to find the requested Boost libraries. > > > Boost version: 1.62.0 > > > Boost include path: /usr/local/BOOST_ROOT/include > > > Could not find the following Boost libraries: > > > boost_serialization > > > Some (but not all) of the required Boost libraries were found. You may > > need to install these additional Boost libraries. Alternatively, set > > BOOST_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT > > to the location of Boost. > > Call Stack (most recent call first): > > CMakeLists.txt:48 (find_package) > > > > -- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.1") > > -- Checking for module 'libvotca_tools' > > -- Found libvotca_tools, version > > -- Checking for module 'sqlite3' > > -- Found sqlite3, version 3.8.10.2 > > -- Found SQLITE3: /usr/lib/libsqlite3.dylib > > -- Found VOTCA_TOOLS: > /Users/Dillon/ProgramBuilds/VOTCA/src/lib/libvotca_tools.dylib > > -- Looking for VotcaToolsFromC in > /Users/Dillon/ProgramBuilds/VOTCA/src/lib/libvotca_tools.dylib > > -- Looking for VotcaToolsFromC in > /Users/Dillon/ProgramBuilds/VOTCA/src/lib/libvotca_tools.dylib - found > > -- Looking for assert.h > > -- Looking for assert.h - found > > -- Looking for C++ include algorithm > > -- Looking for C++ include algorithm - found > > -- Looking for sqrt in m > > -- Looking for sqrt in m - found > > -- Configuring incomplete, errors occurred! > > See also > "/Users/Dillon/ProgramBuilds/VOTCA/src/kmc/CMakeFiles/CMakeOutput.log". > > > On Tuesday, October 4, 2016 at 9:11:15 AM UTC-5, Christoph Junghans wrote: >> >> 2016-10-04 7:00 GMT-06:00 Devon Dillon <devondi...@gmail.com>: >> > I'm having issues with installing csg. Can someone please point me in >> > the >> > right direction? >> > >> > Scanning dependencies of target csg_fmatch_manpage >> > >> > [ 85%] Generating csg_fmatch.man >> > >> > dyld: Library not loaded: libvotca_tools.4.dylib >> > >> > Referenced from: >> > /Users/Dillon/ProgramBuilds/VOTCA/src/csg/src/tools/./csg_fmatch >> > >> > Reason: image not found >> > >> > /bin/sh: line 1: 65933 Trace/BPT trap: 5 ./csg_fmatch --help > >> > csg_fmatch.help >> > >> > make[2]: *** [src/tools/csg_fmatch.man] Error 133 >> > >> > make[1]: *** [src/tools/CMakeFiles/csg_fmatch_manpage.dir/all] Error 2 >> > >> > make[1]: *** Waiting for unfinished jobs >> > >> > [ 86%] Linking CXX executable template_serial >> > >> > [ 86%] Built target template_serial >> > >> > [ 88%] Linking CXX executable template_threaded >> > >> > [ 88%] Built target template_th
Re: [votca] Kirkwood–Buff Integrals for Finite Volumes
2016-10-05 9:46 GMT-06:00 Christoph Junghans <jungh...@votca.org>: > 2016-10-05 1:29 GMT-06:00 Vitalie Botan <vitalie.bo...@gmail.com>: >> Does it have any parameters to play with, like integral cutoff, fudge factor >> etc.? Or in the current version it is all fixed to the values mentioned in >> the paper? > No, the beauty is that C-IBI is parameter-free. > However, you still have the same options as IBI is having, e.g. update > order and scaling factor. C-IBI tutorial and manual section has been added. Christoph > > Christoph >> >> --Vitalie >> >> On Tuesday, October 4, 2016 at 5:19:42 PM UTC+2, Christoph Junghans wrote: >>> >>> >>> See Fig. 8 of http://dx.doi.org/10.1063/1.4947253 for an xml sniplet. >>> We are currently working on a tutorial and a manual update for >>> inclusion in VOTCA 1.4 >>> >>> Christoph >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: The nonbonded interactions couldn't converge with implicit solvent model
2016-09-20 2:11 GMT-06:00 Zidan Zhang <zhangzi...@gmail.com>: > Dear Christoph, > Thank you so much for your advices. > - I have increased the cutoff to 3.0 nm, this time all the rdfs go steadily > to 1, but no obvious improvement can be observed within 52 steps, the plots > in the attachment have the lowest convergence (at 41 step); > - the current system contains 100 decamers (each chain contains 10 > structural units), the box length is 10 nm, and with 6500 solvent molecules > (not water, 2-Butanone), 40 ns NVT simulation, is it big enough? all types > of distributions look smoothly. If the *target* rdf haven't change for a bigger system, you are fine. Christoph > > I will try the rest options. > > Thank you again! > Best regards, > Zidan > > > > On Monday, 19 September 2016 18:15:06 UTC+2, Christoph Junghans wrote: >> >> Some of the rdfs go very abruptly to 1, so you might want to try: >> - increasing the cutoff >> - using a bigger system >> - doing a PBC correction as in http://dx.doi.org/10.1063/1.4742067 >> >> Another option is to >> - add extra exclusion >> - use a fudge factor for the 1-4 interactions >> - adding a couple of special 1-4 interactions >> for that I would split the rdfs in inter-molecular and intra-molecular >> pairs and check if the parts agree to the atomistic case separately. >> >> Christoph >> >> 2016-09-18 3:10 GMT-06:00 Zidan Zhang <zhang...@gmail.com>: >> > The possible reason of mistaken the exclusions can be ignored, I have >> > already checked! >> > >> > >> > On Sunday, 18 September 2016 11:07:09 UTC+2, Zidan Zhang wrote: >> >> >> >> Dear All, >> >> As shown in enclosed material, I prepared a monomer system and a >> >> coresponding decamer system. For the coarse-grained level, I made the >> >> solvent implicit, and using three-beads mapping scheme for each >> >> structural >> >> unit. The IBI for monomer system and for bonded interactions of decamer >> >> system works well, but for the nonbonded interactions of decamer, all >> >> interactions have deviations from their atomistic targets. >> >> I have tried: >> >> 1. using different initial CG configuration; >> >> 2. change the temperature to modify the initial guess of the potential; >> >> 3. scale factor during the iteration; >> >> 4. a five-beads mapping scheme. >> >> All of these couldn't solve the problem, for some cases listed above, >> >> the >> >> decamers in the box get phase separation. >> >> Any suggestions? Thank you very much! >> >> >> >> Best regards, >> >> Zidan >> >> >> >> >> >> >> >> >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: The nonbonded interactions couldn't converge with implicit solvent model
Some of the rdfs go very abruptly to 1, so you might want to try: - increasing the cutoff - using a bigger system - doing a PBC correction as in http://dx.doi.org/10.1063/1.4742067 Another option is to - add extra exclusion - use a fudge factor for the 1-4 interactions - adding a couple of special 1-4 interactions for that I would split the rdfs in inter-molecular and intra-molecular pairs and check if the parts agree to the atomistic case separately. Christoph 2016-09-18 3:10 GMT-06:00 Zidan Zhang <zhangzi...@gmail.com>: > The possible reason of mistaken the exclusions can be ignored, I have > already checked! > > > On Sunday, 18 September 2016 11:07:09 UTC+2, Zidan Zhang wrote: >> >> Dear All, >> As shown in enclosed material, I prepared a monomer system and a >> coresponding decamer system. For the coarse-grained level, I made the >> solvent implicit, and using three-beads mapping scheme for each structural >> unit. The IBI for monomer system and for bonded interactions of decamer >> system works well, but for the nonbonded interactions of decamer, all >> interactions have deviations from their atomistic targets. >> I have tried: >> 1. using different initial CG configuration; >> 2. change the temperature to modify the initial guess of the potential; >> 3. scale factor during the iteration; >> 4. a five-beads mapping scheme. >> All of these couldn't solve the problem, for some cases listed above, the >> decamers in the box get phase separation. >> Any suggestions? Thank you very much! >> >> Best regards, >> Zidan >> >> >> >> > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Pressure correction
2016-10-03 11:31 GMT-06:00 Chang Woon Jang <changwoonj...@gmail.com>: > Dear Votca Users, > > > I have a question about the simple pressure correction method. I have > changed the scaling factor during the IBI to see whether the pressure is > converged or not. Initially, the pressure is getting close to target > pressure, then the pressure is fluctuating about +/- 100 over the target > pressure (1). > >Then, I changed the scaling factor up and down. But the pressure is still > fluctuating over the target pressure somehow. Sometimes, the pressure is > near the target pressure but few iterations later the pressure again > fluctuated. > > Is this normal behavior when you use simple pressure correction method? > Or, Should the pressure converge to the target pressure and fluctuate small > amount near the target pressure? It is not uncommon to have a pressure of 1bar +/- 100 bar for water systems. That has nothing to do with the pressure correction, but the compressibility of the system. This effect has been discussed on this mailing list many times (use search on https://groups.google.com/group/votca) However, I would compare the pressure fluctuation with the atomistic system as well. gmx energy should give you a good estimate for the fluctuation and the error of the pressure. Christoph > > Thank you. > > Best regards, > Changwoon Jang > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Kirkwood–Buff Integrals for Finite Volumes
2016-10-03 15:43 GMT-06:00 Vitalie Botan <vitalie.bo...@gmail.com>: > Dear VOTCA Community, > > this post is primarily addressed to the development team, but could be of > interest for other users. For quite some time now I am struggling with > various sorts of finite-size, phase-space sampling, poor long-ranged RDFs > etc. effects, which all inevitably result in the convergence and more > important quality of CG potentials in dilute polymer solutions. Very > recently I have encountered an interesting paper, which addressed partially > at least one of the issues, namely, numerical instabilities in the > calculation of Kirkwood-Buff integrals (Gij in VOTCA notation). In this > regard I would like to ask how much effort would be required to implement > the finite size correction to Gij from Eq. 7 of dx.doi.org/10.1021/jz301992u > and would it be of any use for KB-IBI and C-IBI methods at all? :) I could > try to implement these corrections myself, but I am not that familiar with > VOTCA source code and C++ language. It is not hard, I guess - you basically have to multiple the g(r)with h(x) from Eq. 7 before line 69 in <https://github.com/votca/csg/blob/master/share/scripts/inverse/postupd_cibi_correction.sh#L69> I would implement that in a similar fashion as <https://github.com/votca/csg/blob/master/share/scripts/inverse/table_switch_border.pl> which put a cos function over a table. Christoph > All regards, > > Vitaly > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Bonds in XML topology for LAMMPS trajectory
2016-10-27 7:12 GMT-06:00 Gustavo Rondina <rond...@gmail.com>: > Hello VOTCA folks, > > Since LAMMPS dump files provide no topological information, I'm doing as > instructed in the manual and using a XML topology. However, I'm not quite > sure how to specify more than one bond of a single type. > > To simplify my question, suppose I have a bead-spring polymer model with 8 > beads per chain (this would be the reference system). My topology XML file > looks like this in this case: > > > > > > > > > > > > > > > > > bondCHAIN:A1 CHAIN:A2 > bondCHAIN:A2 CHAIN:A3 > bondCHAIN:A3 CHAIN:A4 > bondCHAIN:A4 CHAIN:A5 > bondCHAIN:A5 CHAIN:A6 > bondCHAIN:A6 CHAIN:A7 > bondCHAIN:A7 CHAIN:A8 > > > > There is a single bond type in the system, i.e., the bonds A1-A2, A2-A3, > ..., A7-A8, are all of the same type. I've tried to list them in a single > block, however it didn't allow me to do that. What seems to work is > the setup shown above, where multiple blocks all have the same name. > > My intention is to tell that all these bonds are of the same type. Does this > setup work as intended? As I said, it seems to work, but I don't know > whether I'm doing it in the proper way of if it's only working by accident. Jakub, please correct me if I am wrong, but I think the xml topology will just setup the bond. And remember you only need to tell VOTCA that there are bonds in the topology if you want to analyze them or if you need the exclusions. LAMMPS won't know about the information in the xml topology file. To analyze them (using e.g. csg_stat) you will still need to do a 1:1 mapping xml file listing all the bonds you want to average over. Christoph > > My VOTCA version is 1.4_rc1. > > Cheers, > Gustavo > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
[votca] Votca 1.4 released
Dear all, Votca 1.4 was released under the name 'SuperKurt'. The name was chosen due to the occasion of Kurt Kremer's 60th birthday. We would like to use this chance to thank him for his long standing support and for bringing together the core developers of Votca at the Max-Planck-Institute for Polymer Research. Without him Votca would have never happened. Many many changes happened since 1.3.1, most importantly one new iterative method: coordination iterative Boltzmann inversion. In addition, we also added regularization to IMC, a full featured XML Topology Reader and, dihedral support in csg_fmatch. A detailed list of changes can be found here: https://github.com/votca/csg/blob/master/CHANGELOG.md Thanks to everyone, who contributed new features and bug fixes for this release! Details hare ere: https://github.com/votca/csg/graphs/contributors Due to a lack of developers we will NOT fix any bugs in Votca 1.3.X anymore, so we encourage everyone to update and use the new version. Cheers, Christoph -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: Bonds in XML topology for LAMMPS trajectory
2016-10-28 0:20 GMT-06:00 Jakub Krajniak <jkrajn...@gmail.com>: > Dear Gustavo, > >> (...) >> Your reply made me realize that problem with the tab characters. Maybe >> the XML >> parser is getting confused with a mix of tabs and white spaces? >> >> In any case, now it works correctly (as long as only spaces are used). and >> I >> see the proper exclusions when I run csg_dump with --excl. Thank you. >> > > Indeed, the parser for a list of uses only spaces as a separator. > This will be > fixed (issue: https://github.com/votca/csg/issues/195). > Thank you for your comprehensive report. And merged (https://github.com/votca/csg/pull/197). Thanks Jakub for the quick fix! Christoph > > Best, Jakub > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Installing VOTCA on windows
2016-10-20 5:44 GMT-06:00 melika vokhshoori <melikavokhsho...@gmail.com>: > Dear Users, > I have downloaded the VOTCA csg zip file but I have no idea how to install > the software on windows. Does this software even support windows? I am sorry to tell you that we don't support windows. Your best bet will be to use VOTCA through docker (if you have Windows 10) or installing Fedora Linux inside a VM using Virtualbox. Christoph > I would really appreciate your help here. > Thanks, > Melika Vokhshoori > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Bonded Potential
2016-10-14 14:49 GMT-06:00 John Voorehes <goo12...@gmail.com>: > I have recently completed the tutorial for the bonded interactions for > hexane using csg_boltzmann on single molecule of hexane. So it has for > bonded potential, a A-B bond only. However, for my molecule, the beads are > different (for example A-B-C). How could I separate the tabulated potential > for different bonded potential for example A-B and B-C separately using > csg_boltzmann? Sure, you just need to do A-B-C mapping and select A-B and B-C to go into the potential respectively. Something like: tab bond-AB.pot *:bond-AB:* tab bond-BC.pot *:bond-BC:* Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] error in installing votca with gromacs
2016-10-17 9:07 GMT-06:00 <mbu2015...@gmail.com>:
> Hi all,
>
> I am trying to get my head around on to run votca with gromacs input files.
>
> These are the following steps i am following in the installation -
>
> prefix=/usr/local/votca
> sudo mkdir -p ${prefix}/src
> cd ${prefix}/src
> sudo curl -O
> https://raw.githubusercontent.com/votca/buildutil/master/build.sh
> sudo chmod +x build.sh
> sudo ./build.sh --prefix ${prefix} --minimal -DWITH_FFTW=ON -DWITH_GSL=ON
> -ud
> gromacs tools csg
>
> added the following files to by bashrc and bash_profile respectively -
>
> source /usr/local/votca/bin/GMXRC
> source /usr/local/votca/bin/VOTCARC.bash
>
> I am not trying to run the spce tutorial. I generated the tpr file using the
> grompp command and inputs as given the the "atomistic" folder of spce
> tutorial.
> I have also run an mdrun of the same to generate trr and confout.gro files.
>
> When i try mapping -
> csg_map --top topol.tpr --trj confout.gro --out CG-conf.gro --cg water.xml
>
> I get the following error -
> an error occurred:
> input format not supported: topol.tpr
>
> Can someone please tell me where i am going wrong ..
See Sikandar's Email from earlier today, but in short you will have to
add -DWITH_GMX=ON to build.sh command line to get support for tpr
files.
Christoph
>
> Thanks for your time.
>
> --
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--
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Re: [votca] Running votca with lammps
2016-10-24 6:36 GMT-07:00 melika vokhshoori <melikavokhsho...@gmail.com>: > Would you please give a step by step guide on how to run Votca with lammps > and where the Votca code is written and how the environment looks like? Do we > run it on a cmd page? I have downloaded Votca for windows using docker as I > was advised before, the installation seems to have carried out well but I > have no idea where the Votca file is downloaded to. I don't see an icon > saying Votca anywhere. So I am wondering how does this software even work? > How do I get a lammps code ( an atomistic model modelled on lammps) to be > coarse grained by Votca? Votca is a command line only tool and hence there is no icon. The Votca docker container comes with Gromacs (but not LAMMPS), so if might be easier to start with Gromacs. A tutorial on how to do coarse-graining with VOTCA (and Gromacs) can be found here: <https://sites.google.com/a/votca.org/main/tutorials/coarse-graining> Christoph > Sorry for the long text. > Thanks > Melika > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Adding a new C function in csg/src/tool/ in VOTCA
2016-11-02 17:12 GMT-06:00 Mohammad Motevaselian <h.motevasel...@gmail.com>: > Hi, > > So far I have worked with VOTCA to do coarse graining and went through the > structure of the codes and scripts (specifically csg_reupdate.cc and > csg_fmatch.cc). > I want now to implement a new C function in VOTCA. Could you please tell me, > where should I specify the name of my new function, such that cmake > understand > that it exists and compile it. All file named *.cc get compile into , e.g. csg_stat.cc csg_stat_imc.cc csg_stat_imc.h get compile into csg_stat. After adding the file to csg/src/tools you need to re-run cmake. If you need a function in two csg programs, you need to add the file to libcsg (dir csg/src/libcsg) and rerun cmake. Christoph > > thanks > Mohammad > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Gromacs problem with option -tableb
2016-12-16 5:33 GMT-07:00 mhuelsmann via votca <votca@googlegroups.com>: > Hey! > > I'm using Votca for the first time and I'm just trying out the csg-tutorials > which already worked fine for water. > > However, in the case of hexane, when I try to execute an inverse Boltzmann > iteration and a tabulated CG potential > is used, I get a problem with the Gromacs mdrun -tableb option: > > # ERROR: > # > # critical: 'gmx mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc > -tableb table_a1.xvg table_b1.xvg' failed > > When I had a look into the log file, I got the following error message: > > Error in user input: > Invalid command-line options > In command-line option -tableb > Too many values > > Maybe I'm using the wrong Gromacs version (I'm using 5.1.1)? I think you go hit by a bug in gromacs-5.1.1, see: <https://groups.google.com/d/msg/votca/fGgjXpJQqmI/npxPH-2aPQAJ> > > Could anyone help me with this problem? Just upgrade gromacs to 5.1.3 or even to 2016. Christoph > > Thanks a lot! > Marco > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: Converting *.pot.ib to *.xvg
2017-01-12 21:44 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > Thank you for the help. Does it work now? > > On Thursday, January 12, 2017 at 9:34:39 PM UTC-6, Christoph Junghans wrote: >> >> 2017-01-12 10:10 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >> > I am currently using VOTCA v1.3.1 and I took a look at the values of r >> > and I >> > couldn't find repeated values of r. I have attached the files of the >> > resample and the initial file. >> Your function_resample.pot is full of out of range values (3rd column >> is "o"), this must have happened in some early step when working with >> the potential. (see section 3.6 of the manual >> http://votca.github.io/doxygen/manual.pdf) >> >> You can workaround that by telling csg_call ignore the flags using the >> "sloppy-table" option: >> $ csg_call --sloppy-tables table extrapolate function_resample.pot >> table_extrapolate.pot >> >> However, I would do the table conversion like this: >> $ csg_call --options bond.xml --ia-name bond --ia-type bond >> convert_potential gromacs R3-C1-func.pot.ib R3-C1-func.pot.xvg >> with bond.xml (starting from >> >> https://github.com/votca/csg-tutorials/blob/master/hexane/atomistic/bond.xml >> only modifying min and max t 0.3 and 0.46): >> $ cat bond.xml >> >> >> >> bond >> 0.3 >> 0.46 >> 0.01 >> >> >> >> 1e8 >> 2.0 >> 0.002 >> >> >> >> >> Cheers, >> >> Christoph >> > >> > On Thursday, January 12, 2017 at 9:29:33 AM UTC-6, Christoph Junghans >> > wrote: >> >> >> >> 2017-01-11 20:14 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >> >> > Output: >> >> > >> >> > Running subscript 'table_extrapolate.pl function_resample.pot >> >> > function_extra.pot' (from tags table extrapolate) dir >> >> > /usr/local/votca/share/votca/scripts/inverse >> >> > Use of uninitialized value in subtraction (-) at >> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl >> >> > line >> >> > 227. >> >> > Use of uninitialized value in subtraction (-) at >> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl >> >> > line >> >> > 227. >> >> > Use of uninitialized value in subtraction (-) at >> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl >> >> > line >> >> > 227. >> >> > Use of uninitialized value in subtraction (-) at >> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl >> >> > line >> >> > 227. >> >> > Illegal division by zero at >> >> > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl >> >> > line >> >> > 227. >> >> > >> >> > Callstack: >> >> > /usr/local/votca/bin/csg_call - linenumber 199 >> >> > do_external - linenumber 177 in >> >> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh >> >> > die - linenumber 109 in >> >> > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh >> >> > >> >> > >> >> > ## >> >> > # >> >> > # >> >> > # ERROR: >> >> > # >> >> > # do_external: subscript >> >> > # >> >> > # /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl >> >> > function_resample.pot function_extra.pot # >> >> > # (from tags table extrapolate) failed >> >> > # >> >> > # Details can be found above >> >> > # >> >> > # >> >> > # >> >> > >> >> > >> >> > ## >> >> > >> >> > >> >> > On Wednesday, January 11, 2017 at 8:55:41 PM UTC-6, Bijay Shrestha >> >> > wrote: >> >> >> >> >> >> Hi there, >> >> >> I was stuck in the post processing of the potential (to be >> >&
Re: [votca] Re: Converting *.pot.ib to *.xvg
2017-01-11 20:14 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > Output: > > Running subscript 'table_extrapolate.pl function_resample.pot > function_extra.pot' (from tags table extrapolate) dir > /usr/local/votca/share/votca/scripts/inverse > Use of uninitialized value in subtraction (-) at > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl line 227. > Use of uninitialized value in subtraction (-) at > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl line 227. > Use of uninitialized value in subtraction (-) at > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl line 227. > Use of uninitialized value in subtraction (-) at > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl line 227. > Illegal division by zero at > /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl line 227. > > Callstack: > /usr/local/votca/bin/csg_call - linenumber 199 > do_external - linenumber 177 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > die - linenumber 109 in > /usr/local/votca/share/votca/scripts/inverse/functions_common.sh > ## > # > # > # ERROR: > # > # do_external: subscript > # > # /usr/local/votca/share/votca/scripts/inverse/table_extrapolate.pl > function_resample.pot function_extra.pot # > # (from tags table extrapolate) failed > # > # Details can be found above > # > # > # > ## > > > On Wednesday, January 11, 2017 at 8:55:41 PM UTC-6, Bijay Shrestha wrote: >> >> Hi there, >> I was stuck in the post processing of the potential (to be specific on >> the extrapolation of the potential). Firstly, I clipped the irregular >> distributions especially the borders. Then I did the csg_resample and >> obtained the resampled table .pot file. Then when I went for the >> extrapolation using csg_call and got error messages. The command that I gave >> was: >> >> csg_call table extrapolate table_resample.pot \ table_extrapolate.pot >> >> The error message said that was it was dividing by zero and hence couldn't >> proceed. Are there any criteria for the process (because I was able to >> perform the extrapolation of some potential)? What version of VOTCA is this? Looking at line 227 of table_extrapolate.pl: https://github.com/votca/csg/blob/master/share/scripts/inverse/table_extrapolate.pl#L227 it seems the only way to get a division by zero error is if you have repeated r values in the first column of the table. Can you check that? In VOTCA 1.4 you could use $ csg_call --options options.xml --ia-type non-bonded --ia-name X-X convert_potential gromacs instead do to all steps at once. (Search the mailing list for details.) Christoph >> >> Thank you in advance. > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Issues with a charged molecule
2017-03-22 5:55 GMT-06:00 Rom <romnikthi...@gmail.com>: > Hi all :) > > I am working on a system where I have a large charged dye molecule, a > charged counterion, and water as the solvent. > > The atomistic simulations are good, and yet when i force match the > interactions, any interaction with the counterion (counterion-counterion, > dye-counterion etc) all show a force profile of peaks and wells at around > 10^13 and 10^-13! > I thought maybe it was the -rerun part, so I deleted all the charges in my > topology before re-running, since i thought it was the charge that was an > issue, and yet it is still doing this! > > Does anyone know what the problem is? Is there a certain way to deal with > charged molecules when force matching? That is more a question for Sikandar > > Many thanks! > Romnik > > p.s. if you need to look at any files, just let me know so I can attach them > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] methanol tutorial modification
2017-03-15 1:45 GMT-06:00 <mbu2015...@gmail.com>: > Dear votca users. > > I am a new votca user.I am trying to make a two site model for methanol. The > CH3 group is replaced by one bead and OH by another. I have one bonded > interaction and three non-bonded interactions. I am trying to coarse grain > using force matching. I have created a methane.xml and a fmatch.xml file > (attached). After performing an all atom simulation I run the command for > force matching as - > csg_stat --top topol.tpr --trj traj.trr --options fmatch.xml > > But i get the following error - Topology does not have beads of type "CH3" > This was specified in type1 of > interaction "A-B" "CH3" is a coarse-grained name, but you didn't specify a mapping file, try adding "--cg methanol.xml" in the command above. > > Can someone please tell me what is wrong with my input files ? In addition, the block needs to be inside a block, see: <https://github.com/votca/csg-tutorials/blob/master/hexane/atomistic/hexane.xml#L25> > > Also, the manual says min and max for fmatch can be set using csg_dump. Can > someone please tell me who this can be done without any initial guess in the > .xml file ? You mixing something up here, the min and max are set inside the options file (in your case fmatch.xml). Christoph > > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Script table_switch_border.pl
2017-04-12 8:00 GMT-06:00 Javier Ramos <jrdc...@gmail.com>: > Dear all, > > Just a short question, is it possible to call (or set-up) the script > table_switch_border.pl in the settings.xml file when I run csg_inverse > script? No, it is a leftover from the thermodynamic force iteration, which we found could be useful at some point. You will need to write a post update script yourself. See postupd_smooth.sh for an example to start from. Christoph > > Thank you > Javi > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Script table_switch_border.pl
2017-04-21 2:44 GMT-06:00 Christoph Scherer <christophschere...@gmail.com>: > I just checked again, and as far as I remember it is not a leftover from the > thermodynamic force integration, but I implemented it in terms of usind it > with csg_fmatch. It applies a smoothing function of the form y = y*cos( > pi*(x-x_switch)/(2*(x_end-x_switch)) ) to all table values between x_switch > (3rd argument when calling) and the table end and can be called with > csg_call table switch_border. I would recommend to use it at the end of the > iterative process when you have your "final" potential and want a smooth > decay to zero. You are right, you added it here: <https://github.com/votca/csg/commit/0867e81c5d11b9968156f2e4dbcf8cc915075645> Running it at the end of the iteration might be another option, but to call it from csg_call using a option in the settings.xml, a postadd or postupd wrapper needs to be added. Javi, what did you had in mind? Christoph > > > Am Mittwoch, 12. April 2017 18:36:24 UTC+2 schrieb Christoph Junghans: >> >> 2017-04-12 8:00 GMT-06:00 Javier Ramos <jrd...@gmail.com>: >> > Dear all, >> > >> > Just a short question, is it possible to call (or set-up) the script >> > table_switch_border.pl in the settings.xml file when I run csg_inverse >> > script? >> No, it is a leftover from the thermodynamic force iteration, which we >> found could be useful at some point. >> You will need to write a post update script yourself. >> See postupd_smooth.sh for an example to start from. >> >> Christoph >> > >> > Thank you >> > Javi >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Additional Trajectory Loading
2017-04-13 14:34 GMT-06:00 Alireza Moradzadeh <a.mr...@gmail.com>:
> Let me be more specific, for example in relative entropy we can calculate
> average of AA esemble using rdf the second method is to use mapped AA
> trajectory and calculate energy based on trajectory! however, this method is
> not efficient so current implementation uses RDF. however, for parameters in
> my mind I need to have access to energy of each frame of AA trajectory but
> in csg_application we have:
>
>
>_traj_reader =
> TrjReaderFactory().Create(_op_vm["trj"].as ());
> if (_traj_reader == NULL)
> throw runtime_error(string("input format not supported:
> ") + _op_vm["trj"].as ());
> // open the trajectory
> _traj_reader->Open(_op_vm["trj"].as ());
>
>
> and then we use worker and evalconfiguration to calculate different
> properties. Now I want to do similar thing for mapped AA trajectory. I am
> looking for a way to evaluate mapped AA (MAA) and CG in series.
>
> The way that I am seeking which is not efficient is to run csg_xxx.cc once
> for CG save dlamda and d2lamda and then run it again and use saved
> information to evaluate the other trajectory! But it is not efficient and
> systematic. For sure, there is a way to do all these stuff with one run in
> series!
Like I said csg_map does a hybrid topology, which you could use for
analysis in your case:
<https://github.com/votca/csg/blob/master/src/tools/csg_map.cc#L84>
You could even put most of the stuff in the BeginEvaluate() for better
performance.
But by the end of the day, you will have to play a bit around with
code yourself as nobody has done something similar, yet.
Plus, the work might not worth it due to the fact that at most you can
save a factor 2 (in comparison to running your analysis tool twice).
Christoph
>
> Thanks,
> Alireza
>
> On Thursday, April 13, 2017 at 8:43:01 AM UTC-5, Christoph Junghans wrote:
>>
>> 2017-04-12 21:51 GMT-06:00 Alireza Moradzadeh <a.m...@gmail.com>:
>> > Dear All,
>> >
>> > I need to have access to All-Atom MD and Coarse-Grained MD simulations
>> > and
>> > do some calculation based on frames trajectories. Current version of
>> > votca
>> > using csgapplication only loads one trajectory file using
>> > TrajectoryReader *
>> > _traj_reader, However, I need to define another worker and trajectory
>> > reader. I am not sure if I have to change csgapplication or try to
>> > implement
>> > a new thread, worker and evalconfiguration just for my own function
>> > (lets
>> > say csg_xxx.cc) .
>> > In other words, I need to do some calculation on CGMD and AAMD to
>> > calculate
>> > some properties, so I want to have access to both of them in the same
>> > program csg_xxx.cc and I want it to be parallel.
>> >
>> > Any recommendation is highly appreciated!
>> Have a look at the code of csg_map:
>> <https://github.com/votca/csg/blob/master/src/tools/csg_map.cc>
>> and especially on how the "hybrid" option is implemented.
>> This option is using the coarse-grained and atomistic trajectory at
>> the same time.
>>
>> Christoph
>> >
>> > --
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "votca" group.
>> > To unsubscribe from this group and stop receiving emails from it, send
>> > an
>> > email to votca+un...@googlegroups.com.
>> > To post to this group, send email to vo...@googlegroups.com.
>> > Visit this group at https://groups.google.com/group/votca.
>> > For more options, visit https://groups.google.com/d/optout.
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to votca+unsubscr...@googlegroups.com.
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--
Christoph Junghans
Web: http://www.compphys.de
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Re: [votca] Additional Trajectory Loading
2017-04-12 21:51 GMT-06:00 Alireza Moradzadeh <a.mr...@gmail.com>: > Dear All, > > I need to have access to All-Atom MD and Coarse-Grained MD simulations and > do some calculation based on frames trajectories. Current version of votca > using csgapplication only loads one trajectory file using TrajectoryReader * > _traj_reader, However, I need to define another worker and trajectory > reader. I am not sure if I have to change csgapplication or try to implement > a new thread, worker and evalconfiguration just for my own function (lets > say csg_xxx.cc) . > In other words, I need to do some calculation on CGMD and AAMD to calculate > some properties, so I want to have access to both of them in the same > program csg_xxx.cc and I want it to be parallel. > > Any recommendation is highly appreciated! Have a look at the code of csg_map: <https://github.com/votca/csg/blob/master/src/tools/csg_map.cc> and especially on how the "hybrid" option is implemented. This option is using the coarse-grained and atomistic trajectory at the same time. Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] csg_stat force dihedral to be periodic
2017-04-19 13:18 GMT-06:00 Joshua Moore <jdmo...@ncsu.edu>: > Hello, > > During the dihedral measurement using csg_stat, is there a way to force the > distribution to be measured to be periodic? For example, measuring the > histogram at -Pi and adding that to the histogram at Pi? > > Is that with the flag? I think csg_boltzmann supports that flag, but csg_stat does not. You could certainly add that somewhere here: <https://github.com/votca/csg/blob/master/src/tools/csg_stat_imc.cc#L400> Christoph > > Something like this? > > > A_A_A_A_dihedral > 1 > -3.1415 > 3.1415 > 0.05 > > > Thanks. > > Josh > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] csg_inverse terminates without inverse.log
2017-03-03 15:31 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > Did you guys found any mistakes in my file? fyi I have made bonded > interaction tables in table_b1, table_b2, table_a1 xvg files which are > numbered acc to CG topology file. I am supposed to do that instead of > table_A_B.xvg for bonded interaction, right? Gromacs complains there is no table_ALC_CC.xvg, but you only have the CC-ALC interaction in your settings.xml. So I guess, you need to revert the order of "CC ALC" to "ALC CC" in the energygrp_table line of your grompp.mdp. Background here is that gromacs doesn't look for the Y-X table if only the pair X-Y is list in the energygrp_table line. Christoph > > > On Friday, March 3, 2017 at 9:18:02 AM UTC-6, Bijay Shrestha wrote: >> >> I re-ran the csg_inverse. Now it is asking for another file >> table_ALC_CC.xvg. Same as above table_ALC_CC.xvg is the file I want to >> create using csg_inverse. It creates table_CC_ALC.xvg in step_001 as >> suggested in settings.xml. >> >> >> >> CC-ALC >> >> CC >> ALC >> >> 0 >> 1.5 >> 0.01 >> >> >> CC-ALC.dist.tgt >> >> 1 0 0 >> >> >> >> convergence >> >> >> table_CC_ALC.xvg >> >> >> >> >> I have also attached my settings file and inverse.log. >> >> On Friday, March 3, 2017 at 8:44:20 AM UTC-6, Christoph Junghans wrote: >>> >>> 2017-03-02 13:13 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >>> > Currently my error is (as shown in inverse.log) : >>> > >>> > Library file table_CC_DH1.xvg not found in current dir nor in default >>> > directories. >>> > (You can set the directories to search with the GMXLIB path variable) >>> > For more information and tips for troubleshooting, please check the >>> > GROMACS >>> > website at http://www.gromacs.org/Documentation/Errors >>> > >>> > However, this is the file I am trying to calculate using csg_inverse: >>> > My settings files for the interaction looks like: >>> > >>> > >>> > >>> > CC-DH1 >>> > >>> > CC >>> > DH1 >>> > >>> > 0 >>> > 1.5 >>> > 0.01 >>> > >>> > >>> > CC-DH1.dist.tgt >>> > >>> > 1 0 0 >>> > >>> > >>> > >>> > convergence >>> > >>> > >>> > table_CC_DH1.xvg >>> > >>> > >>> > >>> > >>> > What could be problem? And thank you for the support. >>> Looks good so far! >>> >>> Is there a "table_CC_DH1.xvg" in your step_001? Can you attach your >>> inverse.log? >>> >>> Christoph >>> > >>> > On Tuesday, February 28, 2017 at 4:14:47 PM UTC-6, Christoph Junghans >>> > wrote: >>> >> >>> >> 2017-02-28 15:08 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >>> >> > Thank you for the help. It works now. My mistake was in my >>> >> > settings.xml >>> >> > ( I >>> >> > had an extra in the file). However, I also faced >>> >> > another >>> >> > problem. The problem now is that, suppose I have two beads namely A1 >>> >> > and >>> >> > B1. >>> >> > I have given dis.tgt for A1-B1. It is still asking me B1-A1 tables >>> >> > too. >>> >> > Do I >>> >> > need to have both interactions? A1-B1 and B1-A1 interactions >>> >> > mentioned? >>> >> No, you just need one! See the propane example: >>> >> >>> >> >>> >> https://github.com/votca/csg-tutorials/blob/master/propane/ibi/settings.xml >>> >> it only has A-B. >>> >> >>> >> Christoph >>> >> > >>> >> > On Monday, February 27, 2017 at 3:39:09 PM UTC-6, Christoph Junghans >>> >> > wrote: >>> >> >> >>> >> >> 2017-02-27 13:35 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >>> >> >> &g
Re: [votca] Bond Potential Extrapolation
2017-03-10 12:01 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>: > Thanks! > > I had just added that and was going to do a pull request but you beat me to > it. > > That works much better now with that option. > > I was still having an issue though with the extrapolation, so I changed the > bond, angle and torsion extrapolation to the sasha function in > potential_extrapolate.sh. and I'm having a lot less issues now. > > Is it possible to control this option for the extrapolation option from > within the xml? It looked like I could only change it within > potential_extrapolate.sh. Does this work for you: <https://github.com/votca/csg/pull/203> ? > > Thanks. > > Josh > > On Friday, March 10, 2017 at 12:43:01 PM UTC-5, Christoph Junghans wrote: >> >> 2017-03-10 0:05 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>: >> > I am having issues with the bond potential table written during ibi. If >> > I >> > cut it only in the region that should be fit (where the distribution is >> > nonzero), it does not extend far enough for LAMMPS, but if I extend this >> > region in the bonded section, the extrapolation is not steep enough. >> > Please >> > see the attachment. LAMMPS recently changed so if a bond length is >> > outside >> > the table it gives an error. Previously it would just use the force at >> > the >> > end points. >> > >> > Is there an option to set only a specific range, but then extend this >> > when >> > writing the table? >> > >> > Do we need to set the upper and lower end points like the angle >> > potential in >> > potential_to_lammps.sh? It looks like there is an option for Gromacs >> > but >> > not LAMMPS? >> Apparently, there was only a option for lammps, but no >> option (like gromacs has), so I added that: >> >> <https://github.com/votca/csg/commit/c228c63844efe8789cd0242f1f592b0519c3e701> >> >> Christoph >> > >> > >> > >> > A_A_bond >> > 2.0 >> > 8.0 >> > 0.01 >> > >> > >> > A_A_bond.dist.tgt >> > 0 >> > >> > table_b1.pot >> > >> > >> > >> > >> > Thanks. >> > >> > Josh >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: Angle and Dihedral Issues with IBI and LAMMPS
2017-03-07 9:12 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
> Nevermind. That was in my original distribution, so VOTCA was inverting it.
>
> How can you measure the dihedral distribution during the IBI without having
> a discontinuity at the end? Otherwise the dpot would try to include this
> discontinuity.
Sorry, my experience with dihedral interactions are pretty limited.
In the case of gromacs we force the table to be periodic:
https://github.com/votca/csg/blob/master/share/scripts/inverse/table_to_xvg.pl#L99
You might want to copy that part for LAMMPS as well.
Christoph
>
> Do you measure just a bit less than 3.1415?
>
>
> On Tuesday, March 7, 2017 at 10:35:54 AM UTC-5, Joshua Moore wrote:
>>
>> The current calculation is causing a discontinuity in the dihedral at the
>> ends, and I think this is occasionally leading to issues in the simulation,
>> at least I think this is the reason. Please see attached.
>>
>> Do we need to add back in the end calculation as you were mentioning?
>> Maybe that was needed.
>>
>> Thanks.
>>
>> Josh
>>
>>
>>
>>
>>
>> On Saturday, March 4, 2017 at 11:45:23 PM UTC-5, Christoph Junghans wrote:
>>>
>>> 2017-03-04 11:26 GMT-07:00 Joshua Moore <jdm...@ncsu.edu>:
>>> > 1) Angles
>>> >
>>> > I realized I was not using the development version. Sorry about this.
>>> > This
>>> > issue seems to have been corrected in the development version. I'm
>>> > still
>>> > not exactly what the change was to fix this, but it is correct in the
>>> > development version.
>>> >
>>> > 2) Dihedrals
>>> >
>>> > I found two issues
>>> >
>>> > a) In potential_to_lammps.sh, there was a scaling to degrees for the
>>> > "scale"
>>> > step. This seems to be the cause of it dropping points in the
>>> > smoothing
>>> > step. If you remove this being applied to the $bondtype="dihedral",
>>> > this
>>> > issue goes away.
>>> The issue is that the table beginning and ending should be converted
>>> to degrees as well in the case of dihedral potentials. For the "angle"
>>> type this issue doesn't appear as the table always goes from 0 to 180
>>> (both in degrees already.)
>>>
>>> >
>>> > However, there was a second issue related to the units LAMMPS expects
>>> > for
>>> > the dihedral. I originally thought the default was radians, but it
>>> > appears
>>> > it is degrees. We need to add this to table_to_tab.pl so that LAMMPS
>>> > knows
>>> > the table is in radians. Then remove the previous check for dihedrals
>>> > when
>>> > it is scaling.
>>> >
>>> > } elsif ($type eq "dihedral" ) {
>>> > printf(OUTFILE "VOTCA"\n");
>>> > printf(OUTFILE "N %i RADIANS\n\n",$#r+1);
>>> > .
>>> > .
>>> > .
>>> >
>>> > LAMMPS seems to be finicky for the derivative for the dihedrals, and I
>>> > think
>>> > the amount of noise in the distribution is causing an issue for short
>>> > runs
>>> > and LAMMPS is complaining that the dihedral table has inconsistent
>>> > forces.
>>> > I'm assuming VOTCA is generating these from a spline? The issue seems
>>> > to be
>>> > alleviated with longer runs. However, LAMMPS has an option to leave
>>> > off the
>>> > forces for the dihedral table and let LAMMPS calculate them. I'll look
>>> > into
>>> > this some more to see if this helps.
>>> >
>>> > I'll work on a pull request if you agree.
>>> Thanks Josh! Your pull request at
>>> <https://github.com/votca/csg/pull/202> seems to fix the two issues
>>> above.
>>>
>>> Christoph
>>>
>>> >
>>> > Thanks.
>>> >
>>> > Josh
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > On Friday, March 3, 2017 at 9:34:52 PM UTC-5, Joshua Moore wrote:
>>> >>
>>> >> Hello,
>>> >>
>>> >> I am seeing some issues with angle and dihedral translation issues.
>>> >>
>>> >> 1) Angles
>>> >>
>>> >> In the attached ANGLE_ISSUE.PNG, I illustrate the issue.
>>> >
Re: [votca] About the propane tutorial file
2017-03-08 8:46 GMT-07:00 B <goo12...@gmail.com>: > > Hi votca users, > I am currently working on the tutorial for propane. In propane/Atomistic, > there is file, fmatch.xml, which I believe needs to be converted to dist.xml > by removing all the fmatch options, to create file to generate target > distribution using csg_stat. However, my question is in the bonded part of > the xml file. Why is the max for the bonded set to be 0.18 nm; and later in > the ibi, the table for bond (table_b1.xvg) reaches to 0.3 nm (not 0.18 nm)? I think there isn't enough statistics in the region 0.18 to 0.3nm, so to get a useful potential it is more reasonable to extrapolate the potential from 0.18 to 0.3. > Same for the non bonded also (why ibi has max to be 1.36 nm (settings.xml); > and in dist.xml has max is 2.33 nm). It is nice to look a the whole rdf to see it shape, but only do ibi in the interesting region. > Moreover, what does the bonded part in > the dist.xml do for running the ibi? Thank you. You only want to copy these section to the settings.xml file if you want to ibi for the bonded interactions as well. Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: Angle and Dihedral Issues with IBI and LAMMPS
2017-03-04 11:26 GMT-07:00 Joshua Moore <jdmo...@ncsu.edu>:
> 1) Angles
>
> I realized I was not using the development version. Sorry about this. This
> issue seems to have been corrected in the development version. I'm still
> not exactly what the change was to fix this, but it is correct in the
> development version.
>
> 2) Dihedrals
>
> I found two issues
>
> a) In potential_to_lammps.sh, there was a scaling to degrees for the "scale"
> step. This seems to be the cause of it dropping points in the smoothing
> step. If you remove this being applied to the $bondtype="dihedral", this
> issue goes away.
The issue is that the table beginning and ending should be converted
to degrees as well in the case of dihedral potentials. For the "angle"
type this issue doesn't appear as the table always goes from 0 to 180
(both in degrees already.)
>
> However, there was a second issue related to the units LAMMPS expects for
> the dihedral. I originally thought the default was radians, but it appears
> it is degrees. We need to add this to table_to_tab.pl so that LAMMPS knows
> the table is in radians. Then remove the previous check for dihedrals when
> it is scaling.
>
> } elsif ($type eq "dihedral" ) {
> printf(OUTFILE "VOTCA"\n");
> printf(OUTFILE "N %i RADIANS\n\n",$#r+1);
> .
> .
> .
>
> LAMMPS seems to be finicky for the derivative for the dihedrals, and I think
> the amount of noise in the distribution is causing an issue for short runs
> and LAMMPS is complaining that the dihedral table has inconsistent forces.
> I'm assuming VOTCA is generating these from a spline? The issue seems to be
> alleviated with longer runs. However, LAMMPS has an option to leave off the
> forces for the dihedral table and let LAMMPS calculate them. I'll look into
> this some more to see if this helps.
>
> I'll work on a pull request if you agree.
Thanks Josh! Your pull request at
<https://github.com/votca/csg/pull/202> seems to fix the two issues
above.
Christoph
>
> Thanks.
>
> Josh
>
>
>
>
>
> On Friday, March 3, 2017 at 9:34:52 PM UTC-5, Joshua Moore wrote:
>>
>> Hello,
>>
>> I am seeing some issues with angle and dihedral translation issues.
>>
>> 1) Angles
>>
>> In the attached ANGLE_ISSUE.PNG, I illustrate the issue.
>>
>> On step000, the initial angle potential is inverted correctly from the
>> angle distribution. The unit conversion appears to be correct. On step001,
>> it also is translated corrected during the scale, smoothing, extrapolation,
>> interpolation, and shifting steps. However, it appears when the LAMMPS
>> table file is written for the angle, something goes wrong. Here I compare
>> to the initial inversion by hand which is shifted in step000, which accounts
>> for the difference. The smoothing, extrapolation, interpolation steps fall
>> on top of one another, and the shifting step is shifted of course.
>>
>> Again here the issue appears to be the lammps table writing step, although
>> I haven't been able to find the issue in the code. Any ideas?
>>
>> 2) Dihedrals
>>
>> See attached DIHEDRAL_ISSUE.PNG
>>
>> Here, there may very well be a LAMMPS table writing issue as with the
>> angles, but on step001 the first issue that occurs is on the smoothing
>> steps, where it drops most of the data points and fits only 11 points. This
>> is the cause for the difference. This is then populated through to the next
>> steps including writing the LAMMPS table file. Although the smooth,
>> extrapolation, interpolation, and shifting steps are in radians, the scaling
>> step writes the file in degrees, although it appears this is not
>> subsequently used. This scaling step is correct in the translation of the
>> potential and the number of points. The next step I think after this is the
>> smoothing step which again drops most of the points and appears to be the
>> major issue here.
>>
>> I think the dihedral issue might be a general issue in VOTCA and not
>> necessarily a problem with interfacing with LAMMPS?
>>
>>
>> Thanks in advance.
>>
>> Josh
>>
>>
> --
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--
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Web: http://www.compphys.de
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Re: [votca] csg_inverse terminates without inverse.log
2017-03-02 13:13 GMT-07:00 Bijay Shrestha <bijay.shres...@selu.edu>: > Currently my error is (as shown in inverse.log) : > > Library file table_CC_DH1.xvg not found in current dir nor in default > directories. > (You can set the directories to search with the GMXLIB path variable) > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > However, this is the file I am trying to calculate using csg_inverse: > My settings files for the interaction looks like: > > > > CC-DH1 > > CC > DH1 > > 0 > 1.5 > 0.01 > > > CC-DH1.dist.tgt > > 1 0 0 > > > > convergence > > > table_CC_DH1.xvg > > > > > What could be problem? And thank you for the support. Looks good so far! Is there a "table_CC_DH1.xvg" in your step_001? Can you attach your inverse.log? Christoph > > On Tuesday, February 28, 2017 at 4:14:47 PM UTC-6, Christoph Junghans wrote: >> >> 2017-02-28 15:08 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >> > Thank you for the help. It works now. My mistake was in my settings.xml >> > ( I >> > had an extra in the file). However, I also faced another >> > problem. The problem now is that, suppose I have two beads namely A1 and >> > B1. >> > I have given dis.tgt for A1-B1. It is still asking me B1-A1 tables too. >> > Do I >> > need to have both interactions? A1-B1 and B1-A1 interactions mentioned? >> No, you just need one! See the propane example: >> >> https://github.com/votca/csg-tutorials/blob/master/propane/ibi/settings.xml >> it only has A-B. >> >> Christoph >> > >> > On Monday, February 27, 2017 at 3:39:09 PM UTC-6, Christoph Junghans >> > wrote: >> >> >> >> 2017-02-27 13:35 GMT-07:00 Bijay Shrestha <bijay.s...@selu.edu>: >> >> > Hi there, >> >> > I had obtained bonded tabulated potentials for our study molecule >> >> > using >> >> > csg_boltzmann. Then using the tables of bonded potential, I am >> >> > working >> >> > on >> >> > the non-bonded interaction using csg_inverse. For this, I have edited >> >> > the >> >> > settings.xml and grompp.mdp, topol.top of propane tutorial for our >> >> > system. I >> >> > compared my files with the propane systems files for ibi run. >> >> > However, >> >> > when >> >> > I ran the csg_inverse --options settings.xml, it terminates >> >> > (prints"Terminated") without any error message or inverse.log. Could >> >> > you >> >> > help me answering what could I have been missing? >> >> 1.) Does the original tutorial work? (If not it might be a computer >> >> system issue). >> >> 2.) Make sure your settings.xml is a valid xml, check that with >> >> $ xmlwf settings.xml >> >> 3.) Run csg_inverse in debug mode: >> >> $ csg_inverse --debug --options settings.xml >> >> >> >> Christoph >> >> > >> >> > -- >> >> > You received this message because you are subscribed to the Google >> >> > Groups >> >> > "votca" group. >> >> > To unsubscribe from this group and stop receiving emails from it, >> >> > send >> >> > an >> >> > email to votca+un...@googlegroups.com. >> >> > To post to this group, send email to vo...@googlegroups.com. >> >> > Visit this group at https://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
[votca] Re: [votca-ctp] Re: Using ctp_map with non-tpr file creates nigh-empty database
an one type of molecules, instead of associating >>> 3UMB with the residue number 2, it is assigned number 4. >>> >>> I greatly appreciate any further help you can provide. >>> >>> Best, >>> Torsten >>> >>> -- >>> You received this message because you are subscribed to the Google Groups >>> "votca-ctp" group. >>> To unsubscribe from this group and stop receiving emails from it, send an >>> email to votca-ctp+...@googlegroups.com. >>> To post to this group, send email to votc...@googlegroups.com. >>> Visit this group at https://groups.google.com/group/votca-ctp. >>> For more options, visit https://groups.google.com/d/optout. >> >> > -- > You received this message because you are subscribed to the Google Groups > "votca-ctp" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca-ctp+unsubscr...@googlegroups.com. > To post to this group, send email to votca-...@googlegroups.com. > Visit this group at https://groups.google.com/group/votca-ctp. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] forces from the original trajectory
2017-07-27 16:49 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Hello, > I am trying to retrieve pairwise forces from original gromacs trajectory. I > have tried using csg_fmatch with the -no-map tag. I get nan-s for my forces. > Do I have to change the bond/non-bond section in the options xml file in > anyway before I can use fmatch with -no-map? I am not sure if csg_fmatch can actually work without a mapping file. That is more a question for the other Christoph. However, I would run csg_stat with a similar option file first to make sure you got the globbing of the particle types right. Christoph > > Thanks in advance. > > M. Chakraborty > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] how to set "min" and "max" value in settings.xml
2017-08-14 14:28 GMT-06:00 J. Li <jing...@rug.nl>: > Dear all, > > I am new in VOTCA-csg, and trying to read tutorial. When I reading the > settings.xml file, I couldnot understand the way how one decide the values > for "max" and "min" for bonded and/or nonbonded interaction potentials. > Following is an example of settings.xml file Either you have to have good knowledge about the interaction already, or you will to look at its distribution function to see where they have non-zero values. Also see the manual: http://doc.votca.org/manual.pdf Christoph > > > grid > > > > true > > 10 > > > > > bond > > 0.0 > 1.0 > 0.001 > > > > angle > > 0.0 > 3.1415 > 0.01 > > > > > A-A > A > A > 0 > 2.5 > 0.01 > > > > B-B > B > B > 0 > 2 > 0.01 > > > > A-B > A > B > 0 > 2 > 0.01 > > > > Thanks in advance. > > Best regards, > JIng > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] I don't understand this error when I trying to use csg_inverse
2017-08-16 4:09 GMT-06:00 J. Li <jing...@rug.nl>:
> Hello all,
>
> I got error when trying to use csg_inverse in votca-csg. The error is
> following:
>
> #
> # ERROR:
> #
> # run_gromacs.sh: trajectory type (cg.inverse.gromacs.traj) is 'xtc', but
> nstxtcout is 0 in grompp.mdp. Please check the setting again and remove the
> current step. #
> # For details see the logfile
> /home/software/votca/share/votca/csg-tutorials/spce/ibi/inverse.log
>
> In the script, it says:
>
> if [[ $traj == *.xtc ]]; then
> [[ $(get_simulation_setting nstxtcout 0) -eq 0 ]] && die "${0##*/}:
> trajectory type (cg.inverse.gromacs.traj) is '${traj##*.}', but nstxtcout is
> 0 in $mdp. Please check the setting again and remove the current step."
>
> But in the mdp options, it should be nstxout-compressed not nstxtcout. I
> think this is the problem. But I am not sure I am misunderstanding this
> error.
Yeah we fixed that problem recently:
https://github.com/votca/csg/commit/f30763785429c9afa004ecb83ae1dbd538c5a94f
Christoph
>
> Thanks in advance.
> Jing
>
>
>
> --
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--
Christoph Junghans
Web: http://www.compphys.de
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Re: [votca] problems running hexane ibi
2017-08-14 3:05 GMT-06:00 <sufigueroa0...@gmail.com>: > Hi Christoph, thanks a lot, > the installation had actually problems. The administrator of the cluster > reinstalled and now it is working :) > S. Thanks for the update. > > On Friday, 11 August 2017 20:35:57 UTC+2, Christoph Junghans wrote: >> >> 2017-08-11 9:28 GMT-06:00 <sufigue...@gmail.com>: >> > Hello, >> > I am new in Votca. I want to use IBI (csg_inverse --options >> > settings.xml) >> > using the hexane tutorial files (both: ibi_all and also ibi_nonbonded), >> > and >> > everything goes well, starting with the step_000 and then, in the >> > step_001 >> > prepares everything to run the CG simulations with gromacs but, it gets >> > stucked and it is not going further. >> > >> > The last lines that it prints are about the grompp command >> > (from the inverse.log file) it says: >> > >> > csg_get_property: No value for 'cg.inverse.gromacs.log' found in >> > >> > /work/sgerstenmaier/VOTCA/csg-tutorials-master/hexane/ibi_all/settings.xml, >> > trying /opt/share/votca-1.5-dev/share/votca/xml/csg_defaults.xml >> > csg_get_property: returning emtpy value for 'cg.inverse.gromacs.log' >> > Running critical command 'mpirun -np 8 >> > /opt/share/gromacs-5.1.4/bin/gmx_mpi_d grompp -n index.ndx -f grompp.mdp >> > -p >> > topol.top -o topol.tpr -c conf.gro' >> > >> > If I do out of vodca: >> > $gmx_mpi_d grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr >> > -c >> > conf.gro >> > >> > it works properly generating the topol.tpr file. >> > >> > Do you know where is the problem? Thanks, thanks a lot, >> Looks good to me, so far. Can you try calling gmx grompp without >> mpirun, i.e. by setting cg.inverse.gromacs.grompp.bin to >> /opt/share/gromacs-5.1.4/bin/gmx_mpi_d grompp? grompp isn't really >> parallel >> >> Christoph >> > Susana >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] how to set "min" and "max" value in settings.xml
On Aug 17, 2017 03:14, "J. Li" <jing...@rug.nl> wrote: Thanks for your reply, Christoph, Distribution function which has to be looked at is that of the target atomistic simulation? Yes! Christoph Thanks again. Best, Jing On Wednesday, August 16, 2017 at 2:42:05 PM UTC+2, Christoph Junghans wrote: > > 2017-08-14 14:28 GMT-06:00 J. Li <jin...@rug.nl>: > > Dear all, > > > > I am new in VOTCA-csg, and trying to read tutorial. When I reading the > > settings.xml file, I couldnot understand the way how one decide the > values > > for "max" and "min" for bonded and/or nonbonded interaction potentials. > > Following is an example of settings.xml file > Either you have to have good knowledge about the interaction already, > or you will to look at its distribution function to see where they > have non-zero values. Also see the manual: > http://doc.votca.org/manual.pdf > > Christoph > > > > > > grid > > > > > > > > true > > > > 10 > > > > > > > > > > bond > > > > 0.0 > > 1.0 > > 0.001 > > > > > > > > angle > > > > 0.0 > > 3.1415 > > 0.01 > > > > > > > > > > A-A > > A > > A > > 0 > > 2.5 > > 0.01 > > > > > > > > B-B > > B > > B > > 0 > > 2 > > 0.01 > > > > > > > > A-B > > A > > B > > 0 > > 2 > > 0.01 > > > > > > > > Thanks in advance. > > > > Best regards, > > JIng > > > > -- > > You received this message because you are subscribed to the Google > Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an > > email to votca+un...@googlegroups.com. > > To post to this group, send email to vo...@googlegroups.com. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: VOTCA 1.3
2017-07-19 7:35 GMT-06:00 Tudose V <tudose...@gmail.com>: > Thank you for your replay. > > I tried to install but it didn't work. The error message is shown below. > Could you suggest an idea for this problem? As the error message suggested did you look at /home/home/votca13/src/csg/CMakeFiles/CMakeError.log? What does it say at the end? Can you post its content here? Christoph > > Best regards! > Tudose Virgil > > > -- Checking for module 'libgromacs' > -- Found libgromacs, version 5.1.2 > -- Looking for GromacsVersion in /usr/local/gromacs/lib/libgmx.so > -- Looking for GromacsVersion in /usr/local/gromacs/lib/libgmx.so - found > -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/libgmx.so > -- Looking for init_domdec_vsites in /usr/local/gromacs/lib/libgmx.so - not > found > -- Looking for gmx_gpu_sharing_supported in /usr/local/gromacs/lib/libgmx.so > -- Looking for gmx_gpu_sharing_supported in /usr/local/gromacs/lib/libgmx.so > - not found > CMake Error at CMakeModules/FindGROMACS.cmake:50 (message): > Could not find gmx_version, init_domdec_vsites nor > gmx_gpu_sharing_supported in the gromacs library, take look at the error > message in /home/home/votca13/src/csg/CMakeFiles/CMakeError.log to find > out > what was going wrong. This most likely means that your gromacs version is > too old, we need at least gromacs 5 ! > Call Stack (most recent call first): > CMakeLists.txt:88 (find_package) > > -- Configuring incomplete, errors occurred! > See also "/home/home/votca13/src/csg/CMakeFiles/CMakeOutput.log". > See also "/home/home/votca13/src/csg/CMakeFiles/CMakeError.log". > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
[votca] VOTCA Workshop
Dear all, if you are interested in a hands-on tutorial on VOTCA and/or the opportunity to chat with some of the VOTCA developers (I won't make it this year). There is a workshop on "Simulating Soft Matter with ESPResSo, ESPResSo++ and VOTCA" which will take place on October 9-13, 2017 in Stuttgart, Germany Please check the web page for details: <https://www.cecam.org/workshop-1523.html> and don't hesitate to contact us if you have any questions. Cheers, Christoph -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Exclusions to calculate only non-bonded forces
2017-06-08 16:24 GMT-06:00 Christoph Junghans <jungh...@votca.org>: > 2017-06-08 15:56 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: >> Hello, >> >> I was following the hexane hybrid tutorial and there [exclusions] were >> included in the topology file to consider only non-bonded forces for >> subsequent force-matching. I a bit confused about how exclusions work since >> in the GROMACS manual (Chap. 5 Topologies) it is said that the [exclusions] >> section will exclude all the non-bonded interactions between the atom >> indices listed. It sounded like the opposite of what was intended in the >> hybrid hexane. I am clearly missing something. I would appreciate if someone >> can help me to understand it. Thanks. > I guess you are referring to the "fmatch_intramolecular" folder, right? > The exclusions in that topology are made, to then rerun gromacs on the > trajectory without the exclusions. > So basically you end up with forces, which have no contributions from > the bonds, but are calculated on positions generated by the full > interactions set. > See the "Model System and Simulation Details" of > <http://dx.doi.org/10.1002/mats.201100011> for how the subtraction > method works. I meant exclusion method! Christoph > > Christoph >> >> M. Chakraborty >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] VOTCA installation error on Centos
2017-06-20 11:08 GMT-06:00 Christoph Junghans <jungh...@votca.org>: > 2017-06-19 19:15 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: >> Dear Christoph, >> >> The OpenMPI problem has been solved by adding the full path of gfortran to >> f77 and fc in the $HOME/.spack/linux/compilers.yaml file. See >> https://github.com/LLNL/spack/issues/3146 >> >> I am now able to install votca-csg@develop and votca-tools@develop. However, >> during the installation of csg package, the program will produce an error by >> saying something like "can not find libgromacs_d.so". This is because spack >> installed gromacs with enabled mpi but without double precision, thus the >> library name is libgromacs_mpi.so. When copy or rename this file to >> libgromacs_d.so, I am able to install the package without errors. But I >> don't know if this will harm the usage of csg or not since the library is >> not a double precision version. If it does not, a better way (I guess) to >> solve this problem might be add in the source code to let the program find >> either libgromacs_d.so, libgromacs_mpi.so or libgromacs_mpi_d.so, >> corresponding to different gromac versions. > Oh, votca-csg should actually depend on a non-mpi version of gromacs, > here is a fix: > <https://github.com/LLNL/spack/pull/4556/commits/205e2a1fb8ef5eca3710a8381a58507a7035ef6d> > >> >> Another point is that I am wondering if it is possible to specify the >> library path in spack in case we need to use the packages outside spack, >> something like the -DCMAKE_PREFIX_PATH in cmake. > Yeah, just use the path from "spack find -p votca-csg@develop". > >> >> Could you also add votca-ctp and its corresponding packages to spack? maybe >> also TXT2TAG as it is required in some packages in ctp. > I add the votca-ctp in this pull request to spack: > <https://github.com/LLNL/spack/pull/4556> It got merged, so just update your spack version and it should work! Christoph > > Christoph >> >> Thanks a lot >> With best regards, >> Shiyun >> >> 在 2017年6月18日星期日 UTC+8下午6:19:44，Shiyun Xiong写道： >>> >>> Dear Christoph, >>> >>> I found a discussion on this issue in spack at: >>> https://github.com/LLNL/spack/issues/3146 >>> I am not familiar with the solutions provided and I posted a further >>> question below the discussion. >>> >>> Best regards, >>> Shiyun >>> >>> 在 2017年6月17日星期六 UTC+8上午1:09:00，Christoph Junghans写道： >>>> >>>> 2017-06-16 5:55 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >>>> > Dear Christoph, >>>> > >>>> > Thanks a lot for your kind help. Yes, it does not matter the usage of >>>> > the >>>> > software without installing the manual. I was just curious for that. >>>> > With the quota for the two paths in DCMAKE_PREFIX_PATH, it indeed works >>>> > without appearing the warnings. >>>> > The bug of spack has been reported. >>>> Thanks, can you also report the openmpi issue on Centos7. >>>> >>>> Thanks, >>>> >>>> Christoph >>>> > >>>> > Thanks again for the help! >>>> > >>>> > With best regards, >>>> > Shiyun >>>> > >>>> > 在 2017年6月15日星期四 UTC+8下午11:23:14，Christoph Junghans写道： >>>> >> >>>> >> 2017-06-15 6:50 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >>>> >> > Dear Christoph, >>>> >> > >>>> >> > Thanks a lot for you kind help. >>>> >> > >>>> >> > After many tryings, I am now able to install votca with build.sh >>>> >> > except >>>> >> > the >>>> >> > manual. >>>> >> > So the problem should caused by the old versions of many softwares >>>> >> > on >>>> >> > Centos >>>> >> > system. First I uninstalled gcc4.4.7 and deleted all files related >>>> >> > to >>>> >> > all >>>> >> > gcc versions except 6.1.0. The binutils, fftw and cmake packages are >>>> >> > also >>>> >> > reinstalled with the latest version (important for gromacs). >>>> >> > Although votca is successfully installed, there are still several >>>> >> > points >>>> >> > I >>>>
Re: [votca] Dose VOTCA provide back/reverse mapping scheme?
2017-06-21 6:25 GMT-06:00 Jakub Krajniak <jkrajn...@gmail.com>: > Dear Jang, > > As far as I know VOTCA does not provide reverse mapping tool but there are > few methods available on the market that you could try. Jakub is correct, VOTCA doesn't have that functionality. The only related feature is the hybrid mapping of csg_map, which is useful to set up an initial condition to relax from in the backmapping. Christoph > > You can have a look in the following papers: > > 1. Rzepiela, A. J., Louhivuori, M., Peter, C. & Marrink, S. J. Hybrid > simulations: combining atomistic and coarse-grained force fields using > virtual sites. Phys. Chem. Chem. Phys. 13, 10437–48 (2011). > 2. Wassenaar, T. a., Pluhackova, K., Böckmann, R. a., Marrink, S. J. & > Tieleman, D. P. Going Backward: A Flexible Geometric Approach to Reverse > Transformation from Coarse Grained to Atomistic Models. J. Chem. Theory > Comput. 10, 676–690 (2014). > 3. Krajniak, J., Pandiyan, S., Nies, E. & Samaey, G. Generic Adaptive > Resolution Method for Reverse Mapping of Polymers from Coarse-Grained to > Atomistic Descriptions. J. Chem. Theory Comput. 12, 5549–5562 (2016). > 4. Lazutin, a a, Glagolev, M. K., Vasilevskaya, V. V & Khokhlov, a R. > Hypercrosslinked polystyrene networks: an atomistic molecular dynamics > simulation combined with a mapping/reverse mapping procedure. J. Chem. Phys. > 140, 134903 (2014). > 5. Kacar, G., Peters, E. a. J. F. & de With, G. Multi-scale simulations for > predicting material properties of a cross-linked polymer. Comput. Mater. > Sci. 102, 68–77 (2015). > > Best, > Jakub > > > On Wed, Jun 21, 2017 at 11:52 AM, Chang Woon Jang <changwoonj...@gmail.com> > wrote: >> >> Dear Votca users, >> >> I have a question about back mapping tool from CG to atomistic >> representation with VOTCA. >> >> Is this available/possible with VOTCA? >> >> Thank you. >> >> Best regards, >> Changwoon Jang >> >> -- >> You received this message because you are subscribed to the Google Groups >> "votca" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to votca+unsubscr...@googlegroups.com. >> To post to this group, send email to votca@googlegroups.com. >> Visit this group at https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > > > -- > Jakub Krajniak > jkrajniak.pl > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] csg_fmatch segmentation fault in cluster
2017-06-26 7:33 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Hello, > > This is from gdb: > > [Thread debugging using libthread_db enabled] > warning: File "/gpfs/fs1/sfw/gcc/5.3.0/lib64/libstdc++.so.6.0.21-gdb.py" > auto-loading has been declined by your `auto-load safe-path' set to > "/usr/share/gdb/auto-load:/usr/ > lib/debug:/usr/bin/mono-gdb.py". > To enable execution of this file add >add-auto-load-safe-path > /gpfs/fs1/sfw/gcc/5.3.0/lib64/libstdc++.so.6.0.21-gdb.py > line to your configuration file "/home/mchakra2/.gdbinit". > To completely disable this security protection add >set auto-load safe-path / > line to your configuration file "/home/mchakra2/.gdbinit". > For more information about this security protection see the > "Auto-loading safe path" section in the GDB manual. E.g., run from the > shell: >info "(gdb)Auto-loading safe path" > Reading file topol.tpr, VERSION 5.1.3 (single precision) > I have 6000 beads in 1000 molecules > I have 2000 beads in 1000 molecules for the coarsegraining > trn version: GMX_trn_file (single precision) > Reading frame 0 time0.000 > Reading frame 20 time 20.000 Number of spline functions for the > interaction A-A:35 > Number of spline functions for the interaction B-B:35 > Number of spline functions for the interaction A-B:35 > > You are using VOTCA! > > hey, somebody wants to forcematch! > > Using simple Least Squares! > > Program received signal SIGSEGV, Segmentation fault. > 0x2ef1da6a in LAPACKE_dge_nancheck () from > /software/intel/2016.0515/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_lp64.so > Missing separate debuginfos, use: debuginfo-install > expat-2.0.1-11.el6_2.x86_64 glibc-2.12-1.166.el6_7.7.x86_64 > sqlite-3.6.20-1.el6.x86_64 zlib-1.2.3-29.el6.x86_64 > (gdb) bt > #0 0x2ef1da6a in LAPACKE_dge_nancheck () from > /software/intel/2016.0515/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_lp64.so Hmm, that seems to be inside mkl. Can you try to build VOTCA without mkl (option -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON) and use gsl instead to see if the problem persists? Christoph > #1 0x2ef22cb2 in LAPACKE_dgels () from > /software/intel/2016.0515/compilers_and_libraries_2016.3.210/linux/mkl/lib/intel64/libmkl_intel_lp64.so > #2 0x2adaf5fc in > votca::tools::linalg_qrsolve(boost::numeric::ublas::vector<double, > boost::numeric::ublas::unbounded_array<double, std::allocator > >&, > boo > st::numeric::ublas::matrix<double, > boost::numeric::ublas::basic_row_major, > boost::numeric::ublas::unbounded_array<double, std::allocator > >&, > boost::numeric::ublas::vector<double, > boost::numeric::ublas::unbounded_array<double, std::allocator > >&, > boost::numeric::ublas::vector<double, boost::numeric::ubla > s::unbounded_array<double, std::allocator > >*) () from > /software/votca/b2/lib/libvotca_tools.so.5 > #3 0x0040bcd6 in CGForceMatching::FmatchAccumulateData() () > #4 0x0040d0ef in > CGForceMatching::EvalConfiguration(votca::csg::Topology*, > votca::csg::Topology*) () > #5 0x2aaec044 in > votca::csg::CsgApplication::ProcessData(votca::csg::CsgApplication::Worker*) > () from /software/votca/b2/lib/libvotca_csg.so.5 > #6 0x2aaec06a in votca::csg::CsgApplication::Worker::Run() () from > /software/votca/b2/lib/libvotca_csg.so.5 > #7 0x2aaedd8c in votca::csg::CsgApplication::Run() () from > /software/votca/b2/lib/libvotca_csg.so.5 > #8 0x2ad7f05b in votca::tools::Application::Exec(int, char**) () > from /software/votca/b2/lib/libvotca_tools.so.5 > #9 0x0041a1d3 in main () > (gdb) quit > > > Thanks. > > ~M. Chakraborty > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] apply for post to votca group
2017-05-23 3:25 GMT-06:00 Bensen-zjg Zhang <zhangjg2...@gmail.com>: > Dear developers of votca, > > I have some errors when install votca on centos, and seek for help by > posting the error message to votca group. my email account is > zhangjg2...@gmail.com. Thanks in advance! Welcome! Christoph > > Have a nice day. > > Jianguo Zhang > > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] VOTCA installation error on Centos
2017-05-24 2:00 GMT-06:00 Bensen-zjg Zhang <zhangjg2...@gmail.com>: > Dear VOTCA developers and users, > > > I am trying to install the VOTCA software with build.sh on Centos system but > encountered some errors. Before install votca, I have installed all the > dependencies: Boost, Git, GSL, FFTW3, EXPAT, PkgConfig, SQLITE3, Doxygen, > Gromacs. The gcc version is 6.1.0 and the current boost version is 1.53.0. > The installation command I used is: > > ./build.sh --prefix /usr/local/votca/ > -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so --dev tools csg kmc > moo ctp ctp-tutorials ctp-manual > > With this building command, I got the following error information: > /usr/local/lib/libboost_program_options.so: undefined reference to > `std::__cxx11::basic_string<char, std::char_traits, > std::allocator >::~basic_string()@GLIBCXX_3.4.21' Errors like these usually mean your boost has been compiled with an older (ABI-incompatible) version of gcc. (I am guessing so, as you are using gcc-6.1 which relatively recent, while boost-1.53 is actually more than 4 years old.) See the troubleshooting block of https://gcc.gnu.org/onlinedocs/gcc-5.2.0/libstdc++/manual/manual/using_dual_abi.html for details. Just install a newer version of boost using your gcc-6.1 and have VOTCA compile against that one. Christoph > /usr/local/lib/libboost_program_options.so: undefined reference to > `std::logic_error::logic_error(std::__cxx11::basic_string<char, > std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' > /usr/local/lib/libboost_program_options.so: undefined reference to > `std::__cxx11::basic_string<wchar_t, std::char_traits, > std::allocator >::~basic_string()@GLIBCXX_3.4.21' > /usr/local/lib/libboost_program_options.so: undefined reference to `operator > delete(void*, unsigned long)@CXXABI_1.3.9' > /usr/local/lib/libboost_program_options.so: undefined reference to > `std::__cxx11::basic_string<char, std::char_traits, > std::allocator >::_M_replace(unsigned long, unsigned long, char > const*, unsigned long)@GLIBCXX_3.4.21' > /usr/local/lib/libboost_program_options.so: undefined reference to > `std::__cxx11::basic_string<char, std::char_traits, > std::allocator >::find(char const*, unsigned long, unsigned long) > const@GLIBCXX_3.4.21' > /usr/local/lib/libboost_filesystem.so: undefined reference to > `std::__cxx11::basic_string<char, std::char_traits, > std::allocator >::rfind(char, unsigned long) const@GLIBCXX_3.4.21' > collect2: ld returned 1 exit status > make[2]: *** [src/tools/votca_property] Error 1 > make[1]: *** [src/tools/CMakeFiles/votca_property.dir/all] Error 2 > make: *** [all] Error 2 > > When searching from the previous discussions, I found that I may need to > specify the Boost path. As a result, I tried: > > ./build.sh --prefix /usr/local/votca/ > -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so > -DBoost_INCLUDE_DIR=/usr/local/include/boost/ > -DBoost_PROGRAM_OPTIONS_LIBRARY=/usr/local/lib/libboost_program_options.so > -DBoost_FILESYSTEM_LIBRARY=/usr/local/lib/libboost_filesystem.so --dev tools > csg kmc moo ctp ctp-tutorials ctp-manual > > > This time, votca can not find the boost package? I have no idea why it can > not find boost since I have specified the path to it! > For more information, I have attached the entire on screen printed > information and the cmake error file. The file names with "_noBoostPath" > correspond to the first building command (no boost path is specified) while > the file names with "_withBoostPath" correspond to the second building > command. > > By the way, when using the second building command, votca find both GSL and > MKL libraries, so I have also tried to disable the mkl library with > -DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON, but not change happens. > > Thank you very much for your kind help! > With best regards, > Shiyun > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] VOTCA installation error on Centos
2017-05-26 4:23 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > I have install the latest BOOST version 1.64.0. However, I have encountered > other errors: 'Make_array' is not a member of 'boost::serialization'. Yup, boost 1.64.0 has a bug (see here: <https://svn.boost.org/trac/boost/ticket/12516>), which has nothing to do with VOTCA. 1.64 is very new release and hence not very well tested. > In fact, I have used this version of BOOST at the beginning and this error > occured. Denis suggested me to downgrade my boost version and I found from > the votca website that 1.53 is a recommanded version. That's why I used 1.53 Ok, let me try to clarify. VOTCA works pretty much works with any gcc and boost version (except may the above mentioned boost-1.64.0). However, VOTCA (from version 1.4on ) uses C++-11 features and hence depends on C++-11 ABI. Unfortunately, <=gcc-4.9, gcc-5* and >=gcc-6 have 3 different C++-11 ABIs and hence you will get the "undefined reference" error from above when trying to link VOTCA against a boost, which was built with a different C++-11 ABI. There are multiple solutions to that issue: 1.) Use the system (NOT /usr/local) gcc and boost - usually the Linux distributions get their thing together nicely. 2.) Use a (non-buggy) boost version, which is compiled with SAME compiler as you are compiling VOTCA with. 3.) If you don't need the development version of VOTCA, just use the package, which comes with your linux distributions - OpenSuse, Fedora, Debian, Ubuntu have VOTCA packages. See <https://github.com/votca/csg/wiki/Installing> Christoph > > Attached are the on screen information and cmake error information. Please > check it. Thank you so much! > > Best regards, > Shiyun > > > 在 2017年5月24日星期三 UTC+8下午9:53:25，Christoph Junghans写道： >> >> 2017-05-24 2:00 GMT-06:00 Bensen-zjg Zhang <zhang...@gmail.com>: >> > Dear VOTCA developers and users, >> > >> > >> > I am trying to install the VOTCA software with build.sh on Centos system >> > but >> > encountered some errors. Before install votca, I have installed all the >> > dependencies: Boost, Git, GSL, FFTW3, EXPAT, PkgConfig, SQLITE3, >> > Doxygen, >> > Gromacs. The gcc version is 6.1.0 and the current boost version is >> > 1.53.0. >> > The installation command I used is: >> > >> > ./build.sh --prefix /usr/local/votca/ >> > -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ >> > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so --dev tools csg >> > kmc >> > moo ctp ctp-tutorials ctp-manual >> > >> > With this building command, I got the following error information: >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> > `std::__cxx11::basic_string<char, std::char_traits, >> > std::allocator >::~basic_string()@GLIBCXX_3.4.21' >> Errors like these usually mean your boost has been compiled with an >> older (ABI-incompatible) version of gcc. >> (I am guessing so, as you are using gcc-6.1 which relatively recent, >> while boost-1.53 is actually more than 4 years old.) >> >> See the troubleshooting block of >> >> https://gcc.gnu.org/onlinedocs/gcc-5.2.0/libstdc++/manual/manual/using_dual_abi.html >> for details. >> >> Just install a newer version of boost using your gcc-6.1 and have >> VOTCA compile against that one. >> >> Christoph >> >> >> >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> > `std::logic_error::logic_error(std::__cxx11::basic_string<char, >> > std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> > `std::__cxx11::basic_string<wchar_t, std::char_traits, >> > std::allocator >::~basic_string()@GLIBCXX_3.4.21' >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> > `operator >> > delete(void*, unsigned long)@CXXABI_1.3.9' >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> > `std::__cxx11::basic_string<char, std::char_traits, >> > std::allocator >::_M_replace(unsigned long, unsigned long, char >> > const*, unsigned long)@GLIBCXX_3.4.21' >> > /usr/local/lib/libboost_program_options.so: undefined reference to >> > `std::__cxx11::basic_string<char, std::char_traits, >> > std::allocator >::find(char const*, unsigned long, unsigned long) >> > const@GLIBCXX_3.4.21' >> > /usr/local/lib/libboost_filesystem.so: undefined reference to >> > `std::__cxx1
Re: [votca] Using the topology file generated by csg_gmxtopol to run CG simulation in gromacs
2017-05-24 18:58 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Thank you for your prompt response. I have attached the cgtop.top file. I > was trying to figure out what to add to the . top file and added the > [defaults] segment. The initial output from csg_gmxtopol started from > [moleculetype]. Thanks again. I think, there is an "[ atomtypes ]" block missing before "[ moleculetype ]", just have a look at any coarse-grained topol.top in the tutorials, e.g. <https://github.com/votca/csg-tutorials/blob/master/propane/ibi/topol.top#L16>. Christoph > > On Wednesday, 24 May 2017 17:08:13 UTC-4, Christoph Junghans wrote: >> >> 2017-05-24 14:11 GMT-06:00 M. Chakraborty <maghe...@gmail.com>: >> > I am trying to use the tabulated potential (for non-bonded interactions) >> > obtained from force-matching to run coarse-grained simulation in >> > gromacs. To >> > obtain the topology file I have used csg_gmxtopol. conf_cg.gro file was >> > obtained by running csg_map. In order to use the tabulated potential for >> > simulation, I have made the following changes to the mdp file: >> > vdwtype = User >> > coulombtype = User >> > energygrps = A B >> > energygrp_table = A A B B >> > >> > >> > I must mention here that I have mapped methanol molecules into >> > coarse-grained particles having two beads representation (A for CH3 and >> > B >> > for OH). When I run the command, gmx grompp -v -f cg_grompp.mdp -p >> > cgtop.top >> > -c conf_cg.gro, I get the following error: >> > Fatal error: >> > Syntax error - File cgtop.top, line 4 >> > Last line read: >> > '[ moleculetype ]' >> > Invalid order for directive moleculetype >> > >> > I am not sure what is going on here. I am attempting to run a >> > coarse-grained >> > simulation for the first time. It would be really helpful if someone can >> > guide me to identify what is wrong with my approach. >> The output of csg_gmxtopol is only meant as a template and "File still >> needs to be modified by the user" (from --help output). >> >> Can you post your cgtop.top and we might be able to help? >> >> Christoph >> >> > >> > Thank You. >> > >> > M. Chakraborty >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] VOTCA installation error on Centos
2017-05-26 21:02 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks a lot for providing the solutions. > For the first point of using the system gcc and boost: my system gcc > (/usr/bin/gcc) version is 4.4.7 released in 2012, hence it is rather old. > Also, I can not find (I don't know) where is the system boost header files > although I can find the system boost library is in the /usr/lib64/ fold. > Most importantly, as mentioned in my first post, when the boost paths are > specified during the votca installation, it says can not find the required > boost package. As a result, I haven't try this solution! Yes, gcc-4.4.7 would also not support C++11, gcc-4.8 is the first one supporting enough of it to compile VOTCA. > > The second method of using another boost version with the same gcc compiler > as votca: I actually using the default gcc to compile both Boost and Votca > (which gcc --> /usr/local/bin/gcc gcc --version --> gcc (GCC) 6.1.0). So > I think the gcc used to compile both BOOST and votca is the same. Using the > default gcc, I now installed the BOOST 1.62.0 version. However, the > "undefined reference" error still appears. For gcc 6.1, I checked it support > the c++11 standard. Something seems broken here, if you are lucky $ strings -a /path/to/libboost_program_options.so | grep GCC will reveal to you, which gcc was used to compile boost. But I would try to recompile boost in another directory using gcc-6.1 I recently added votca to spack, so you might have a chance to install it that way: <https://github.com/votca/csg/wiki/Installing#spack> Christoph > > For the third one: my system is Centos, it seems there is not votca install. > > Best Regards, > Shiyun > > > 在 2017年5月27日星期六 UTC+8上午12:22:32，Christoph Junghans写道： >> >> 2017-05-26 4:23 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> > Dear Christoph, >> > >> > I have install the latest BOOST version 1.64.0. However, I have >> > encountered >> > other errors: 'Make_array' is not a member of 'boost::serialization'. >> Yup, boost 1.64.0 has a bug (see here: >> <https://svn.boost.org/trac/boost/ticket/12516>), which has nothing to >> do with VOTCA. 1.64 is very new release and hence not very well >> tested. >> >> > In fact, I have used this version of BOOST at the beginning and this >> > error >> > occured. Denis suggested me to downgrade my boost version and I found >> > from >> > the votca website that 1.53 is a recommanded version. That's why I used >> > 1.53 >> Ok, let me try to clarify. VOTCA works pretty much works with any gcc >> and boost version (except may the above mentioned boost-1.64.0). >> >> However, VOTCA (from version 1.4on ) uses C++-11 features and hence >> depends on C++-11 ABI. Unfortunately, <=gcc-4.9, gcc-5* and >=gcc-6 >> have 3 different C++-11 ABIs and hence you will get the "undefined >> reference" error from above when trying to link VOTCA against a boost, >> which was built with a different C++-11 ABI. >> >> There are multiple solutions to that issue: >> 1.) Use the system (NOT /usr/local) gcc and boost - usually the Linux >> distributions get their thing together nicely. >> 2.) Use a (non-buggy) boost version, which is compiled with SAME >> compiler as you are compiling VOTCA with. >> 3.) If you don't need the development version of VOTCA, just use the >> package, which comes with your linux distributions - OpenSuse, Fedora, >> Debian, Ubuntu have VOTCA packages. See >> <https://github.com/votca/csg/wiki/Installing> >> >> Christoph >> >> > >> > Attached are the on screen information and cmake error information. >> > Please >> > check it. Thank you so much! >> > >> > Best regards, >> > Shiyun >> > >> > >> > 在 2017年5月24日星期三 UTC+8下午9:53:25，Christoph Junghans写道： >> >> >> >> 2017-05-24 2:00 GMT-06:00 Bensen-zjg Zhang <zhang...@gmail.com>: >> >> > Dear VOTCA developers and users, >> >> > >> >> > >> >> > I am trying to install the VOTCA software with build.sh on Centos >> >> > system >> >> > but >> >> > encountered some errors. Before install votca, I have installed all >> >> > the >> >> > dependencies: Boost, Git, GSL, FFTW3, EXPAT, PkgConfig, SQLITE3, >> >> > Doxygen, >> >> > Gromacs. The gcc version is 6.1.0 and the current boost version is >> >> > 1.53.0. >> >> > The installati
Re: [votca] Force on CG particles
2017-05-30 21:37 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > I am interested in simulating 2 site coarse-grained representation of > methanol. In order to compare how forces are preserved in the > CG-representation and the all-atom simulation, I have mapped the all-atom > trajectory into CGtraj.xtc using the following command: > csg_map --top topol.tpr --trj traj.trr --out CGTraj.xtc --force --cg > methanol.xml > > I did mention nstfout in the gromacs mdp file for the all-atom simulation. > When I try extracting the forces from the trajectory file with the command: > gmx traj -f CGTraj.xtc -b 100 -of CGforce.xvg -pbc > > I get the following error: > Fatal error: > Cannot extract velocities or forces since your input XTC file does not > contain them. > > I am not sure what I am missing here. I am attaching the xml file. Thanks. xtc files only store positions, you will need to use a trr file as output for csg_map. Christoph > > ~M. Chakraborty > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Force on CG particles
2017-05-31 8:06 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Since force matching uses the atom trajectory to compute tabulated forces, I > am wondering if csg_fmatch can be used to get a list of forces derived from > the all-atom trajectory but mapped to the coarse-grained particles. I tried No, csg_fmatch cannot do that. csg_fmatch do force matching, meaning it will give you the force table, so that the forces deviate the least (in a least square sense) from the average force on each particle (type and average over the whole trajectory). > using the --traj-force option for fmatch but it gave an io error. The > description of the --trj-force flag (coarse-grained trajectory containing > forces of already known interactions) is not very clear to me. The manual > does not talk about it in detail either. Initially I tried mapping the The " --trj-force" is part of the hybrid force matching approach, see: <http://dx.doi.org/10.1002/mats.201100011> For information, see <https://groups.google.com/d/msg/votca/gY2qbyvjlMA/y7Gwsysl84oJ> and here: <https://github.com/votca/csg-tutorials/tree/master/hexane/hybrid_force_matching> Basically, it allows you to subtract forces before force matching. > all-atom traj to cg traj using csg_map. But when I am using gmx traj to > extract the forces, the file lists 6000 (fine grain) atom indices instead of > 2000 (coarse grain). Have you generate a new tpr for the coarse-grained topology? By default "gmx traj" will open topol.tpr, which might not be the right topology. You will need to execute gmx like: $ gmx traj -s CGtopol.tpr -f CGTraj.xtc -b 100 -of CGforce.xvg -pbc Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Issue with pbc
2017-06-02 13:16 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > This might me be more of a gromacs problem but still I am posting it here. I > ran a CG simulation of methanol where I have used two bead representation > for each methanol molecule. I have used force-matching to generate tabulated > potential. I have used almost the same grompp.mdp file as found in the > methanol tutorial (I only added the groups and added constraints to the > bonds). Even though I had set pbc as xyz, when I viewed my trajectory I saw > many of the particles going outside the box. I am not sure why pbc is not > working. I have added my cg_grompp.mdp and cg topology file. You can use "gmx trjconv -pbc mol" to make a trajectory with molecules whole concerning to pbc or "gmx trjconv -pbc atom" to make trajectory with atoms whole concerning to pbc. Christoph > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Issue with pbc
2017-06-05 7:20 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Thanks for your reply. However, my problem is not broken atoms/molecules. I > expect to see broken molecules at the boundary when pbc is set. But for my > simulation, the molecules are intact but they are moving beyond the box > even though pbc is set. Sorry, I should have explained myself a bit better. With "gmx trjconv -pbc atom" you should be able to fold all coordinates back into the 1st image of the simulation box. However, I am not sure why you would want that, any thermodynamics for the trajectory will need to be calculated using minimum image convention anyhow, so having some atom sticking out won't hurt. Christoph > > On Friday, 2 June 2017 18:23:05 UTC-4, Christoph Junghans wrote: >> >> 2017-06-02 13:16 GMT-06:00 M. Chakraborty <maghe...@gmail.com>: >> > This might me be more of a gromacs problem but still I am posting it >> > here. I >> > ran a CG simulation of methanol where I have used two bead >> > representation >> > for each methanol molecule. I have used force-matching to generate >> > tabulated >> > potential. I have used almost the same grompp.mdp file as found in the >> > methanol tutorial (I only added the groups and added constraints to the >> > bonds). Even though I had set pbc as xyz, when I viewed my trajectory I >> > saw >> > many of the particles going outside the box. I am not sure why pbc is >> > not >> > working. I have added my cg_grompp.mdp and cg topology file. >> You can use "gmx trjconv -pbc mol" to make a trajectory with molecules >> whole concerning to pbc or "gmx trjconv -pbc atom" to make trajectory >> with atoms whole concerning to pbc. >> >> Christoph >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an >> > email to votca+un...@googlegroups.com. >> > To post to this group, send email to vo...@googlegroups.com. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Exclusions to calculate only non-bonded forces
2017-06-08 15:56 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Hello, > > I was following the hexane hybrid tutorial and there [exclusions] were > included in the topology file to consider only non-bonded forces for > subsequent force-matching. I a bit confused about how exclusions work since > in the GROMACS manual (Chap. 5 Topologies) it is said that the [exclusions] > section will exclude all the non-bonded interactions between the atom > indices listed. It sounded like the opposite of what was intended in the > hybrid hexane. I am clearly missing something. I would appreciate if someone > can help me to understand it. Thanks. I guess you are referring to the "fmatch_intramolecular" folder, right? The exclusions in that topology are made, to then rerun gromacs on the trajectory without the exclusions. So basically you end up with forces, which have no contributions from the bonds, but are calculated on positions generated by the full interactions set. See the "Model System and Simulation Details" of <http://dx.doi.org/10.1002/mats.201100011> for how the subtraction method works. Christoph > > M. Chakraborty > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] VOTCA installation error on Centos
2017-06-09 5:43 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks for your suggestions and I am sorry for the late reply: I was > travelling last two weeks and were not able to try your suggestions. > > When running strings -a /path/to/libboost_program_options.so | grep GCC, I > got: > GCC_3.0 > GCC: (GNU) 4.4.7 20120313 (Red Hat 4.4.7-11) > GCC: (GNU) 6.1.0 > _Unwind_Resume@@GCC_3.0 > Does this means my boost is not installed by gcc-6.1? I don't why it shows > several versions of gcc. Even when I compile the boost with ./bootstrap.sh > --with-toolset=gcc, ./b2 --toolset=gcc-6.1.0, I got the same information. It seems like it is build with gcc-6.1, I guess. > > Also, you recommended me to install boost in another directory, but in this > case, votca can not find the boost package even when I specified the path of > boost header files and libraries as I mention before. Do you have any ideas > on why this happens? It depends on your cmake version how to override the Boost search path, look for the documentation in the FindBoost.cmake coming with your cmake installation. The latest version uses BOOSTROOT or BOOST_ROOT: <https://gitlab.kitware.com/cmake/cmake/blob/master/Modules/FindBoost.cmake#L42> I am not 100% sure if these are cmake variables or just environment variables. As an alternative you could use CMAKE_PREFIX_PATH as well! > > The spack option has also been tried, while I also did not success to > install votca-csg. The corresponding on screen information and log files are > attached. Besides, it seems votca-ctp is not involved in spack (I tried to > append votca-ctp after the commend but it says it can not find the votca-ctp > package), while this is actually the one I needed. I can add votca-ctp to spack as well if needed. Any how you got hit by <https://github.com/votca/csg/issues/209> again: To overcome this install the development version using spack: $ spack install votca-csg@develop votca-tools@develop Christoph > > Your further help is greatly appreciated. > Best regards, > Shiyun > > > 在 2017年5月28日星期日 UTC+8上午5:24:27，Christoph Junghans写道： >> >> 2017-05-26 21:02 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> > Dear Christoph, >> > >> > Thanks a lot for providing the solutions. >> > For the first point of using the system gcc and boost: my system gcc >> > (/usr/bin/gcc) version is 4.4.7 released in 2012, hence it is rather >> > old. >> > Also, I can not find (I don't know) where is the system boost header >> > files >> > although I can find the system boost library is in the /usr/lib64/ fold. >> > Most importantly, as mentioned in my first post, when the boost paths >> > are >> > specified during the votca installation, it says can not find the >> > required >> > boost package. As a result, I haven't try this solution! >> Yes, gcc-4.4.7 would also not support C++11, gcc-4.8 is the first one >> supporting enough of it to compile VOTCA. >> > >> > The second method of using another boost version with the same gcc >> > compiler >> > as votca: I actually using the default gcc to compile both Boost and >> > Votca >> > (which gcc --> /usr/local/bin/gcc gcc --version --> gcc (GCC) 6.1.0). >> > So >> > I think the gcc used to compile both BOOST and votca is the same. Using >> > the >> > default gcc, I now installed the BOOST 1.62.0 version. However, the >> > "undefined reference" error still appears. For gcc 6.1, I checked it >> > support >> > the c++11 standard. >> Something seems broken here, if you are lucky >> $ strings -a /path/to/libboost_program_options.so | grep GCC >> will reveal to you, which gcc was used to compile boost. >> >> But I would try to recompile boost in another directory using gcc-6.1 >> >> I recently added votca to spack, so you might have a chance to install >> it that way: >> <https://github.com/votca/csg/wiki/Installing#spack> >> >> Christoph >> > >> > For the third one: my system is Centos, it seems there is not votca >> > install. >> > >> > Best Regards, >> > Shiyun >> > >> > >> > 在 2017年5月27日星期六 UTC+8上午12:22:32，Christoph Junghans写道： >> >> >> >> 2017-05-26 4:23 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> >> > Dear Christoph, >> >> > >> >> > I have install the latest BOOST version 1.64.0. However, I have >> >> > encountered >> >> > other errors: 'Make_array' is not a member of 'b
Re: [votca] VOTCA installation error on Centos
2017-06-12 6:46 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks so much for your kind help. Sorry I still have problems. > When using the develop version, there is an error when installing the > openmpi package. It seems that the gcc version it used is not my default > version of 6.1.0 but 4.4.7. Even though I replace the /usr/bin/gcc with my > 6.1.0 version, the same thing happens. The on screen file and the log file > is attached. > > On the other hand, I am also trying to install votca in another cluster > (RedHat). I first installed gcc-6.3.0 and set it as the default gcc version. > However, when I use spack to intall votca, it also stoped on openmpi > installation again. But on this cluster, it says can not find the Fortran > compile! When installing gcc, I have enable the fortran language and also > linked gfortran to /usr/bin/gfortran. When using "gfortran --version" and > "gcc --version", it does appear the correct version I installed. I don't > know why this happens. I have also attached the on screen information as > onScreenInfo_Redhat.txt. The log file is empty so I did not attached it. If it fails building OpenMPI, that is really more a question for the spack mailing list: <https://groups.google.com/d/forum/spack> or its issue tracker: <https://github.com/LLNL/spack/issues> Christoph > > THanks a lot. > Shiyun > > 在 2017年6月9日星期五 UTC+8下午10:59:47，Christoph Junghans写道： >> >> 2017-06-09 5:43 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> > Dear Christoph, >> > >> > Thanks for your suggestions and I am sorry for the late reply: I was >> > travelling last two weeks and were not able to try your suggestions. >> > >> > When running strings -a /path/to/libboost_program_options.so | grep GCC, >> > I >> > got: >> > GCC_3.0 >> > GCC: (GNU) 4.4.7 20120313 (Red Hat 4.4.7-11) >> > GCC: (GNU) 6.1.0 >> > _Unwind_Resume@@GCC_3.0 >> > Does this means my boost is not installed by gcc-6.1? I don't why it >> > shows >> > several versions of gcc. Even when I compile the boost with >> > ./bootstrap.sh >> > --with-toolset=gcc, ./b2 --toolset=gcc-6.1.0, I got the same >> > information. >> It seems like it is build with gcc-6.1, I guess. >> >> > >> > Also, you recommended me to install boost in another directory, but in >> > this >> > case, votca can not find the boost package even when I specified the >> > path of >> > boost header files and libraries as I mention before. Do you have any >> > ideas >> > on why this happens? >> It depends on your cmake version how to override the Boost search >> path, look for the documentation in the FindBoost.cmake coming with >> your cmake installation. >> The latest version uses BOOSTROOT or BOOST_ROOT: >> >> <https://gitlab.kitware.com/cmake/cmake/blob/master/Modules/FindBoost.cmake#L42> >> I am not 100% sure if these are cmake variables or just environment >> variables. >> >> As an alternative you could use CMAKE_PREFIX_PATH as well! >> >> > >> > The spack option has also been tried, while I also did not success to >> > install votca-csg. The corresponding on screen information and log files >> > are >> > attached. Besides, it seems votca-ctp is not involved in spack (I tried >> > to >> > append votca-ctp after the commend but it says it can not find the >> > votca-ctp >> > package), while this is actually the one I needed. >> I can add votca-ctp to spack as well if needed. >> Any how you got hit by <https://github.com/votca/csg/issues/209> again: >> To overcome this install the development version using spack: >> $ spack install votca-csg@develop votca-tools@develop >> >> Christoph >> > >> > Your further help is greatly appreciated. >> > Best regards, >> > Shiyun >> > >> > >> > 在 2017年5月28日星期日 UTC+8上午5:24:27，Christoph Junghans写道： >> >> >> >> 2017-05-26 21:02 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> >> > Dear Christoph, >> >> > >> >> > Thanks a lot for providing the solutions. >> >> > For the first point of using the system gcc and boost: my system gcc >> >> > (/usr/bin/gcc) version is 4.4.7 released in 2012, hence it is rather >> >> > old. >> >> > Also, I can not find (I don't know) where is the system boost header >> >> > files >> >> > although I can find
Re: [votca] VOTCA installation error on Centos
2017-05-26 21:02 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks a lot for providing the solutions. > For the first point of using the system gcc and boost: my system gcc > (/usr/bin/gcc) version is 4.4.7 released in 2012, hence it is rather old. > Also, I can not find (I don't know) where is the system boost header files > although I can find the system boost library is in the /usr/lib64/ fold. > Most importantly, as mentioned in my first post, when the boost paths are > specified during the votca installation, it says can not find the required > boost package. As a result, I haven't try this solution! > > The second method of using another boost version with the same gcc compiler > as votca: I actually using the default gcc to compile both Boost and Votca > (which gcc --> /usr/local/bin/gcc gcc --version --> gcc (GCC) 6.1.0). So > I think the gcc used to compile both BOOST and votca is the same. Using the > default gcc, I now installed the BOOST 1.62.0 version. However, the > "undefined reference" error still appears. For gcc 6.1, I checked it support > the c++11 standard. > > For the third one: my system is Centos, it seems there is not votca install. Centos7 now has a votca package: <https://github.com/votca/csg/wiki/Installing#centos-7> Christoph > > Best Regards, > Shiyun > > > 在 2017年5月27日星期六 UTC+8上午12:22:32，Christoph Junghans写道： >> >> 2017-05-26 4:23 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> > Dear Christoph, >> > >> > I have install the latest BOOST version 1.64.0. However, I have >> > encountered >> > other errors: 'Make_array' is not a member of 'boost::serialization'. >> Yup, boost 1.64.0 has a bug (see here: >> <https://svn.boost.org/trac/boost/ticket/12516>), which has nothing to >> do with VOTCA. 1.64 is very new release and hence not very well >> tested. >> >> > In fact, I have used this version of BOOST at the beginning and this >> > error >> > occured. Denis suggested me to downgrade my boost version and I found >> > from >> > the votca website that 1.53 is a recommanded version. That's why I used >> > 1.53 >> Ok, let me try to clarify. VOTCA works pretty much works with any gcc >> and boost version (except may the above mentioned boost-1.64.0). >> >> However, VOTCA (from version 1.4on ) uses C++-11 features and hence >> depends on C++-11 ABI. Unfortunately, <=gcc-4.9, gcc-5* and >=gcc-6 >> have 3 different C++-11 ABIs and hence you will get the "undefined >> reference" error from above when trying to link VOTCA against a boost, >> which was built with a different C++-11 ABI. >> >> There are multiple solutions to that issue: >> 1.) Use the system (NOT /usr/local) gcc and boost - usually the Linux >> distributions get their thing together nicely. >> 2.) Use a (non-buggy) boost version, which is compiled with SAME >> compiler as you are compiling VOTCA with. >> 3.) If you don't need the development version of VOTCA, just use the >> package, which comes with your linux distributions - OpenSuse, Fedora, >> Debian, Ubuntu have VOTCA packages. See >> <https://github.com/votca/csg/wiki/Installing> >> >> Christoph >> >> > >> > Attached are the on screen information and cmake error information. >> > Please >> > check it. Thank you so much! >> > >> > Best regards, >> > Shiyun >> > >> > >> > 在 2017年5月24日星期三 UTC+8下午9:53:25，Christoph Junghans写道： >> >> >> >> 2017-05-24 2:00 GMT-06:00 Bensen-zjg Zhang <zhang...@gmail.com>: >> >> > Dear VOTCA developers and users, >> >> > >> >> > >> >> > I am trying to install the VOTCA software with build.sh on Centos >> >> > system >> >> > but >> >> > encountered some errors. Before install votca, I have installed all >> >> > the >> >> > dependencies: Boost, Git, GSL, FFTW3, EXPAT, PkgConfig, SQLITE3, >> >> > Doxygen, >> >> > Gromacs. The gcc version is 6.1.0 and the current boost version is >> >> > 1.53.0. >> >> > The installation command I used is: >> >> > >> >> > ./build.sh --prefix /usr/local/votca/ >> >> > -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ >> >> > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so --dev tools >> >> > csg >> >> > kmc >> >> > moo ctp ctp-tutorials ctp-manual >>
Re: [votca] VOTCA installation error on Centos
2017-06-15 6:50 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks a lot for you kind help. > > After many tryings, I am now able to install votca with build.sh except the > manual. > So the problem should caused by the old versions of many softwares on Centos > system. First I uninstalled gcc4.4.7 and deleted all files related to all > gcc versions except 6.1.0. The binutils, fftw and cmake packages are also > reinstalled with the latest version (important for gromacs). > Although votca is successfully installed, there are still several points I > am not clear: > i) When installing the ctp-manual, an error "txt2tags wrote > /home/xiong/votca/ctp-manual/reference/programs/kmc_ru.tex > txt2tags: Error: Cannot read file: ctp_tools.t2t" That is a question for votca-ctp mailing list, but honestly you don't really need the manual to use ctp. And older version can be found in files section of: <http://www.votca.org/Documentation/charge-transport> > > ii) When install votca with the command > ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp > ctp-tutorials -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include/ > -DGROMACS_LIBRARY=/usr/local/gromacs/lib64/libgromacs_mpi_d.so > it successfully compiled but gave a warning: >Manually-specified variables were not used by the project: >FFTW3_INCLUDE_DIR >FFTW3_LIBRARY >GROMACS_INCLUDE_DIR >GROMACS_LIBRARY Well, FFTW3 variable are only needed to build tools and GROMACS variables are only needed to build csg. So, when building kmc moo ctp this warning will show up. You could build tools first and then csg and then the rest to avoid the warnings. > if I change the command to > ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp > ctp-tutorials -DCMAKE_PREFIX_PATH=/usr/local/fftw_shared;/usr/local/gromacs/ I guess you forgot quotes around the two paths: ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp ctp-tutorials -DCMAKE_PREFIX_PATH="/usr/local/fftw_shared;/usr/local/gromacs/" > > It says "Could NOT find GROMACS (missing: GROMACS_LIBRARY > GROMACS_INCLUDE_DIR GROMACS_VERSION)" > but if I use the command: ./build.sh --prefix /usr/local/votca/ --dev tools > csg kmc moo ctp ctp-tutorials -DCMAKE_PREFIX_PATH=/usr/local/fftw_shared > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include/ > -DGROMACS_LIBRARY=/usr/local/gromacs/lib64/libgromacs_mpi_d.so > > the fftw problem can be solved but gromacs is still not used. > > iii) When using spack to install votca, it seems we need the GitHub account > and passport of votca! No that is not true, votca is pull from the https://github.com/votca/tools (see <https://github.com/LLNL/spack/blob/develop/var/spack/repos/builtin/packages/votca-tools/package.py#L39>) which can be used anonymously (without an Github account). Again, this seems to be a bug in Spack, which you should report here: https://github.com/LLNL/spack/issues Honestly, if Votca-1.4 is enough for you, do: <https://github.com/votca/csg/wiki/Installing#centos-7> and install only votca-ctp and moo on top of it using build.sh. Christoph > > Thanks a lot > Best regards, > Shiyun > > > > 在 2017年6月13日星期二 UTC+8下午10:29:26，Christoph Junghans写道： >> >> 2017-06-12 6:46 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> > Dear Christoph, >> > >> > Thanks so much for your kind help. Sorry I still have problems. >> > When using the develop version, there is an error when installing the >> > openmpi package. It seems that the gcc version it used is not my default >> > version of 6.1.0 but 4.4.7. Even though I replace the /usr/bin/gcc with >> > my >> > 6.1.0 version, the same thing happens. The on screen file and the log >> > file >> > is attached. >> > >> > On the other hand, I am also trying to install votca in another cluster >> > (RedHat). I first installed gcc-6.3.0 and set it as the default gcc >> > version. >> > However, when I use spack to intall votca, it also stoped on openmpi >> > installation again. But on this cluster, it says can not find the >> > Fortran >> > compile! When installing gcc, I have enable the fortran language and >> > also >> > linked gfortran to /usr/bin/gfortran. When using "gfortran --version" >> > and >> > "gcc --version", it does appear the correct version I installed. I don't >> > know why this happens. I have also attached the on screen information as &
Re: [votca] VOTCA installation error on Centos
2017-06-16 5:55 GMT-06:00 Shiyun Xiong <s.y.xiong...@gmail.com>: > Dear Christoph, > > Thanks a lot for your kind help. Yes, it does not matter the usage of the > software without installing the manual. I was just curious for that. > With the quota for the two paths in DCMAKE_PREFIX_PATH, it indeed works > without appearing the warnings. > The bug of spack has been reported. Thanks, can you also report the openmpi issue on Centos7. Thanks, Christoph > > Thanks again for the help! > > With best regards, > Shiyun > > 在 2017年6月15日星期四 UTC+8下午11:23:14，Christoph Junghans写道： >> >> 2017-06-15 6:50 GMT-06:00 Shiyun Xiong <s.y.xi...@gmail.com>: >> > Dear Christoph, >> > >> > Thanks a lot for you kind help. >> > >> > After many tryings, I am now able to install votca with build.sh except >> > the >> > manual. >> > So the problem should caused by the old versions of many softwares on >> > Centos >> > system. First I uninstalled gcc4.4.7 and deleted all files related to >> > all >> > gcc versions except 6.1.0. The binutils, fftw and cmake packages are >> > also >> > reinstalled with the latest version (important for gromacs). >> > Although votca is successfully installed, there are still several points >> > I >> > am not clear: >> > i) When installing the ctp-manual, an error "txt2tags wrote >> > /home/xiong/votca/ctp-manual/reference/programs/kmc_ru.tex >> > txt2tags: Error: Cannot read file: ctp_tools.t2t" >> That is a question for votca-ctp mailing list, but honestly you don't >> really need the manual to use ctp. >> And older version can be found in files section of: >> <http://www.votca.org/Documentation/charge-transport> >> >> > >> > ii) When install votca with the command >> > ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp >> > ctp-tutorials -DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/ >> > -DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include/ >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib64/libgromacs_mpi_d.so >> > it successfully compiled but gave a warning: >> >Manually-specified variables were not used by the >> > project: >> >FFTW3_INCLUDE_DIR >> >FFTW3_LIBRARY >> >GROMACS_INCLUDE_DIR >> >GROMACS_LIBRARY >> Well, FFTW3 variable are only needed to build tools and GROMACS >> variables are only needed to build csg. >> So, when building kmc moo ctp this warning will show up. >> You could build tools first and then csg and then the rest to avoid >> the warnings. >> >> > if I change the command to >> > ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp >> > ctp-tutorials >> > -DCMAKE_PREFIX_PATH=/usr/local/fftw_shared;/usr/local/gromacs/ >> I guess you forgot quotes around the two paths: >> ./build.sh --prefix /usr/local/votca/ --dev tools csg kmc moo ctp >> ctp-tutorials >> -DCMAKE_PREFIX_PATH="/usr/local/fftw_shared;/usr/local/gromacs/" >> >> > >> > It says "Could NOT find GROMACS (missing: GROMACS_LIBRARY >> > GROMACS_INCLUDE_DIR GROMACS_VERSION)" >> > but if I use the command: ./build.sh --prefix /usr/local/votca/ --dev >> > tools >> > csg kmc moo ctp ctp-tutorials -DCMAKE_PREFIX_PATH=/usr/local/fftw_shared >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include/ >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib64/libgromacs_mpi_d.so >> > >> > the fftw problem can be solved but gromacs is still not used. >> > >> > iii) When using spack to install votca, it seems we need the GitHub >> > account >> > and passport of votca! >> No that is not true, votca is pull from the https://github.com/votca/tools >> (see >> >> <https://github.com/LLNL/spack/blob/develop/var/spack/repos/builtin/packages/votca-tools/package.py#L39>) >> which can be used anonymously (without an Github account). >> Again, this seems to be a bug in Spack, which you should report here: >> https://github.com/LLNL/spack/issues >> >> Honestly, if Votca-1.4 is enough for you, do: >> <https://github.com/votca/csg/wiki/Installing#centos-7> >> and install only votca-ctp and moo on top of it using build.sh. >> >> Christoph >> > >> > Thanks a lot >> > Best regards, >> > Shiyun >> > >> &g
Re: [votca] Including user defined atom types in index.ndx file
2017-05-25 9:51 GMT-06:00 M. Chakraborty <maghesre...@gmail.com>: > Hello, > I am trying run a coarse-grained simulation of methanol. I am using a two > bead representation of methanol (A- CH3, B- OH). When I ran grompp I > encountered the following error: > > > Fatal error: > Group A referenced in the .mdp file was not found in the index file. > Group names must match either [moleculetype] names or custom index group > names, in which case you must supply an index file to the '-n' option > of grompp. > > I consulted the hexane and propane tutorials, and realized that I have to > provide an index file while running grompp. However, gmx make_ndx -f > conf_cg.gro g gives me an index.ndx file where indices of [A] and [B] are > not listed. I am wondering if I am missing a special directive during the > make_ndx command or do I actually have to add the two blocks of [A] and [B] > indices myself. I am adding my conf_cg.gro and cgtop.top file for > reference. Thanks. When running make_ndx, you need to make a group "A" and "B", e.g. using "a A*" and then "name 3 A" for the "A" group. Christoph > > Regards, > M. Chakraborty > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] Re: two site CG model for methanol
2017-05-30 22:36 GMT-06:00 <mbu2015...@gmail.com>: > I have used only the non-bonded interactions. My reference RDFs (attached) > do not show any bonded interactions, but the RDFs obtained on performing IBI > shows a sharp peak at lower distances > corresponding to bond distributions (attached). Why is this happening ? > Where am I going wrong ? You are missing some exclusions, see here (and the link therein) <https://groups.google.com/d/msg/votca/mtQV1sVSIBA/XvaTXap8BQAJ> on how to fix it. Christoph > > On Monday, May 29, 2017 at 8:27:41 PM UTC+5:30, mbu20...@gmail.com wrote: >> >> Hi, >> >> I am trying to extend the methanol single site tutorial to get two site CG >> model. I keep getting domain decomposition error when >> I try to run IBI on this sytem. I have attached the mapping - methanol.xml >> and setting - setting.xml files and the distribution files. >> Can someone please tell me where I am going wrong and how i can correct >> for this error ... >> >> Thanks > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] possible bug in csg_dump
2017-10-03 3:45 GMT-06:00 Albert Solernou <a.soler...@gmail.com>:
> Hi Christoph,
> if you have a closer look at csgDump_interface, you'll see that masses are
> always fine, but atom types and residue numbers become messed up in the
> "List of molecules" section. Line 184 says:
> 2 Name 3:GLN:CA Type H Mass 12.01 Resnr 2 Resname GLN
You can just do:
$ gmx dump -s nvt-100_interface.tpr | less
and look for the atoms block, you will find:
atom[ 2]={type= 2, typeB= 2, ptype=Atom, m= 1.20100e+01,
q=-3.1e-03, mB= 1.20100e+01, qB=-3.1e-03, resind=2,
atomnumber= 6}
That pretty much matches up with the above line, looking in the
"residue" block below:
residue[2]={name="GLN", nr=32, ic=' '}
So the residue name is correct, too.
The only thing VOTCA does differently is that it start numbering from
1, while gromacs internally starts with 0, hence "3:GLN:CA" (and not
"2:GLN:CA").
> a clear example of a wrong type. Then, if you move down to line 708, a
> valine residue has the residue number wrong too.
> 526 Name 141:VAL:N Type CT Mass 14.01 Resnr 140 Resname VAL
Again:
atom[ 526]={type= 8, typeB= 8, ptype=Atom, m= 1.40100e+01,
q=-4.15700e-01, mB= 1.40100e+01, qB=-4.15700e-01, resind= 140,
atomnumber= 7}
and
residue[140]={name="VAL", nr=73, ic=' '}
Do I miss something here?
Christoph
> 527 Name 142:VAL:H Type HC Mass 1.008 Resnr 141 Resname VAL
> 528 Name 143:VAL:CA Type HC Mass 12.01 Resnr 142 Resname VAL
> 529 Name 144:VAL:HA Type C Mass 1.008 Resnr 143 Resname VAL
> 530 Name 145:VAL:CB Type O Mass 12.01 Resnr 144 Resname VAL
> 531 Name 146:VAL:HB Type N Mass 1.008 Resnr 145 Resname VAL
> 532 Name 147:VAL:CG1 Type H Mass 12.01 Resnr 146 Resname VAL
> 533 Name 148:VAL:HG11 Type H Mass 1.008 Resnr 147 Resname VAL
> 534 Name 149:VAL:HG12 Type C Mass 1.008 Resnr 148 Resname VAL
> 535 Name 150:VAL:HG13 Type O Mass 1.008 Resnr 149 Resname VAL
> 536 Name 151:VAL:CG2 Type N Mass 12.01 Resnr 150 Resname VAL
> 537 Name 152:VAL:HG21 Type H Mass 1.008 Resnr 151 Resname VAL
> 538 Name 153:VAL:HG22 Type CT Mass 1.008 Resnr 152 Resname VAL
> 539 Name 154:VAL:HG23 Type H1 Mass 1.008 Resnr 153 Resname VAL
> 540 Name 155:VAL:C Type CT Mass 12.01 Resnr 154 Resname VAL
> 541 Name 156:VAL:O Type HC Mass 16 Resnr 155 Resname VAL
>
> I will try to reproduce the error with a smaller selection of atoms, though
> I am pretty busy until the 16th Oct. Notes on how to reproduce the error
> were attached previously, and should not be complicated to follow.
>
> I don't know how to interpret the large amount of lines that "gmx dump"
> prints out, so to check that its output is correct:
> - you could check that with the previously attached .tpr
> - I could follow some instructions on how to use "gmx dump".
>
>
> Best,
> Albert
>
> On Sunday, October 1, 2017 at 7:45:10 PM UTC+1, Christoph Junghans wrote:
>>
>> Albert,
>>
>> 2017-10-01 3:20 GMT-06:00 Albert Solernou <a.sol...@gmail.com>:
>> > Hi Cristoph,
>> > thanks for your reply, and for pointing to the code, and sorry I forgot
>> > to
>> > attach the messy output. It is now attached, as well as the conflicting
>> > .tpr
>> > obtained just following the previous notes.
>> >
>> > It would be great to know what do you think of it.
>> Sorry, but what kind of output are you expecting? In your
>> "csgDump_interface" atomtypes seem to be consistent with the atom
>> names, same for the masses.
>>
>> And have you checked that "gmx dump" outputs the right number?
>>
>> Plus, could you make a simple system with just 2 residues exhibit the
>> same misbehavior? (That would be easier to us to debug.)
>>
>>
>> Christoph
>> >
>> > Thanks,
>> > Albert
>> >
>> >
>> >
>> > On Friday, September 29, 2017 at 9:58:06 PM UTC+1, Christoph Junghans
>> > wrote:
>> >>
>> >> Hi Albert,
>> >>
>> >> 2017-09-28 6:24 GMT-06:00 Albert Solernou <a.sol...@gmail.com>:
>> >> > Hi All,
>> >> > I think that there is a bug in csg_dump, as it dumps wrong atom types
>> >> > and
>> >> > some wrong numbers when working with some modified tpr files.
>> >> Can you be a bit more explicit which numbers are wrong?
>> >>
>> >> >
>> >> > Not sure how much the bug affects my work, but feel I should report
>> >> > it
>> >> > anyway. I attach clear instructions on how to get the bug, as well as
>> >> > two
>> >> > inpu
Re: [votca] VOTCA with LAMMPS
2017-10-03 7:58 GMT-06:00 Sudeep Maheshwari <sudeep.posit...@gmail.com>: > Dear Christoph > > Thanks a lot for your reply and hints > I was able to build VOTCA successfully > I used sqlite3 because i want to perform ctp and xtp calculations > I have one more question, for running the ibi_lammps example in > csg_tutorials/spce > I am trying to supply the location of my lammps executable in the > settings.xml but i think i am making a mistake there > I want to use the lmp_mpi executable to run my jobs in parallel > > I am writing it like this > > > > 2.49435 > > > /home/smaheshwari/lammpspimd/lammps-17Nov16/src/lmp_mpi The program is still "lammps". Program has to be "gromacs", "lammps" or something like that. > > You need to add /home/smaheshwari/lammpspimd/lammps-17Nov16/src/lmp_mpi in the block here, see Section 10.4 (pg 55) of <http://votca.github.io/doxygen/manual.pdf> Christoph > > spce.in > > topol.xml > > traj.dump > > > > Could you please point out what is the mistake that i am making > > sincerely > sudeep > > On Monday, October 2, 2017 at 7:13:17 PM UTC+2, Christoph Junghans wrote: >> >> 2017-10-02 4:08 GMT-06:00 Sudeep Maheshwari <sudeep@gmail.com>: >> > I found the web page showing the commands to force search locations, i >> > am >> > able to include commands for the location of SQLITE but the GROMACS is >> > installed as a module which works when i load it using "module load >> > gromacs" >> > on the cluster. >> > Also after even after specifying the locations for the directory of >> > sqlite, >> > the program is not able to detect it and shuts out with the error of No >> > package sqlite3 found. >> > >> > Could you please suggest me some solution of both of these problems >> > I am using the command ./build.sh --prefix ~/votca --dev >> > -DSQLITE_INCLUDE_DIR=/home/smaheshwari/bin/include >> > -DSQLITE_LIBRARY=/home/smaheshwari/bin/lib -DWITH_GMX=OFF tools csg kmc >> > moo >> > ctp ctp-tutorials ctp-manual >> If don't need ctp, you also don't need sqlite3 as well and can disable >> it with the "-DWITH_SQLITE3=OFF" option, csg works without sqlite3. >> >> If you need ctp, you will need to add >> -DSQLITE3_INCLUDE_DIR="/home/smaheshwari/bin/include" and >> -DSQLITE3_LIBRARY="/home/smaheshwari/bin/lib/libsqlite3.so" >> Please note, that we are requiring sqlite3 for ctp and hence both >> variables are called SQLITE3 (note the "3"), and cmake wants >> SQLITE3_LIBRARY to be that path to the library, incl. the library name >> itself. >> >> You can use cmake-gui to see all variables: >> $ export CMAKE=cmake-gui >> $ ./build.sh --prefix ~/votca --dev >> >> For more hints see: https://github.com/votca/csg/wiki/Installing >> >> Christoph >> > >> > sudeep >> > >> > >> > On Monday, October 2, 2017 at 11:06:23 AM UTC+2, Sudeep Maheshwari >> > wrote: >> >> >> >> Thanks a lot for the reply christoph >> >> >> >> I am facing some more problem in compiling VOTCA, as compiling without >> >> sqlite3 is not working and i figured out that i might need gromacs >> >> somewhere >> >> down the line >> >> >> >> Could you please tell me how to force search location for gromacs and >> >> sqlite3 while building votca. >> >> >> >> I was trying the following command but now i want to specify location >> >> of >> >> gromacs and sqlite3 while building >> >> ./build.sh --prefix ~/votca --dev -DWITH_GMX=OFF tools csg kmc moo ctp >> >> ctp-tutorials ctp-manual >> >> >> >> cheers >> >> sudeep >> >> >> >> On Friday, September 29, 2017 at 11:04:49 PM UTC+2, Christoph Junghans >> >> wrote: >> >>> >> >>> Sudeep, >> >>> >> >>> >> >>> >> >>> 2017-09-29 9:02 GMT-06:00 Sudeep Maheshwari <sudeep@gmail.com>: >> >>> > Hello All >> >>> > >> >>> > I am new to installing and using VOTCA. We dont use Gromacs in our >> >>> > group and >> >>> > i have to make VOTCA work with LAMMPS. >> >>> > Could someone please point out how to use build.sh to make Votca on >> >>&
Re: [votca] Installation on an off-line server
2017-10-10 8:54 GMT-06:00 Takahiro Ohkuma <takakuma1...@gmail.com>: > I need to install VOTCA on a computer (RedHat) which is not connecting to > the internet. Could anyone tell me a way to manually install the packages? > Thank you very much for your advice in advance. build.sh has the "--selfdownload" option, just put all the tarball, e.g. votca-tools-1.4.1.tar.gz, votca-csg-1.4.1.tar.gz, in same directory and run build.sh. Otherwise here are some hints on manual install: <https://github.com/votca/csg/wiki/Installing#manual-install> Christoph > > Takahiro > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to votca+unsubscr...@googlegroups.com. > To post to this group, send email to votca@googlegroups.com. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
Re: [votca] possible bug in csg_dump
Albert,
2017-10-13 3:50 GMT-06:00 Albert Solernou <a.soler...@gmail.com>:
> Hi Cristoph,
> I am afraid your answer does not fully address the point. See the comments
> inlined, please.
>
> On Tuesday, October 3, 2017 at 8:34:46 PM UTC+1, Christoph Junghans wrote:
>>
>> 2017-10-03 3:45 GMT-06:00 Albert Solernou <a.sol...@gmail.com>:
>> > Hi Christoph,
>> > if you have a closer look at csgDump_interface, you'll see that masses
>> > are
>> > always fine, but atom types and residue numbers become messed up in the
>> > "List of molecules" section. Line 184 says:
>> > 2 Name 3:GLN:CA Type H Mass 12.01 Resnr 2 Resname GLN
>> You can just do:
>> $ gmx dump -s nvt-100_interface.tpr | less
>> and look for the atoms block, you will find:
>> atom[ 2]={type= 2, typeB= 2, ptype=Atom, m= 1.20100e+01,
>> q=-3.1e-03, mB= 1.20100e+01, qB=-3.1e-03, resind=2,
>> atomnumber= 6}
>> That pretty much matches up with the above line,
>
>
> When I said I don't understand "gmx dump", I meant I do not know how you go
> from here to a PDB line. The error that is showing csg_dump, in the
> previous line is that 3:GLN:CA is not Type H. That is the most important
> thing that I think you should look up.
Ok, I see what you mean!
VOTCA's identifier scheme is ::, so the last
part is the atomname not the atomtype. Atomtypes would make for a
unique identifier string.
However look again at the output of "gmx dump" I see:
atom[2]={name="CA"}
So VOTCA basically just picks up the name from inside the tpr, which
is obviously the wrong name, but there isn't much we can do about
that.
>
>>
>> looking in the
>> "residue" block below:
>> residue[2]={name="GLN", nr=32, ic=' '}
>> So the residue name is correct, too.
>
>
> Yes, the residue name is correct. I always said that it was numbering and
> atom types.
>>
>>
>> The only thing VOTCA does differently is that it start numbering from
>> 1, while gromacs internally starts with 0, hence "3:GLN:CA" (and not
>> "2:GLN:CA").
>>
>> > a clear example of a wrong type. Then, if you move down to line 708, a
>> > valine residue has the residue number wrong too.
>> > 526 Name 141:VAL:N Type CT Mass 14.01 Resnr 140 Resname VAL
>> Again:
>> atom[ 526]={type= 8, typeB= 8, ptype=Atom, m= 1.40100e+01,
>> q=-4.15700e-01, mB= 1.40100e+01, qB=-4.15700e-01, resind= 140,
>> atomnumber= 7}
>> and
>> residue[140]={name="VAL", nr=73, ic=' '}
>>
>> Do I miss something here?
>
>
> Yes, here you miss that the residue number goes crazy and that every atom in
> this region has belongs to a different VAL, while in reality that is not the
> case. However, I see that this is the numbering that spits "gmx dump", so
> that should not be your bug, if I understood your comment correctly,
Yeah I would ask on the gmx developer list
(gmx-develop...@gromacs.org) about this odd behavior. It seems to me
something in your pre-processing went wrong.
Christoph
>
>
> Thanks,
> Albert
>>
>> Christoph
>>
>> > 527 Name 142:VAL:H Type HC Mass 1.008 Resnr 141 Resname VAL
>> > 528 Name 143:VAL:CA Type HC Mass 12.01 Resnr 142 Resname VAL
>> > 529 Name 144:VAL:HA Type C Mass 1.008 Resnr 143 Resname VAL
>> > 530 Name 145:VAL:CB Type O Mass 12.01 Resnr 144 Resname VAL
>> > 531 Name 146:VAL:HB Type N Mass 1.008 Resnr 145 Resname VAL
>> > 532 Name 147:VAL:CG1 Type H Mass 12.01 Resnr 146 Resname VAL
>> > 533 Name 148:VAL:HG11 Type H Mass 1.008 Resnr 147 Resname VAL
>> > 534 Name 149:VAL:HG12 Type C Mass 1.008 Resnr 148 Resname VAL
>> > 535 Name 150:VAL:HG13 Type O Mass 1.008 Resnr 149 Resname VAL
>> > 536 Name 151:VAL:CG2 Type N Mass 12.01 Resnr 150 Resname VAL
>> > 537 Name 152:VAL:HG21 Type H Mass 1.008 Resnr 151 Resname VAL
>> > 538 Name 153:VAL:HG22 Type CT Mass 1.008 Resnr 152 Resname VAL
>> > 539 Name 154:VAL:HG23 Type H1 Mass 1.008 Resnr 153 Resname VAL
>> > 540 Name 155:VAL:C Type CT Mass 12.01 Resnr 154 Resname VAL
>> > 541 Name 156:VAL:O Type HC Mass 16 Resnr 155 Resname VAL
>> >
>> > I will try to reproduce the error with a smaller selection of atoms,
>> > though
>> > I am pretty busy until the 16th Oct. Notes on how to reproduce the error
>> > were attached previously, and should not be complicated to follow.
>> >
>> > I don't know how to interpret the large amount of lines that "gmx dump"
>> > prints out, so to check that its
