On Thu, May 3, 2018 at 1:46 PM, Alex <[email protected]> wrote:
>
> On Thu, May 3, 2018 at 3:03 PM, Christoph Junghans <[email protected]>
> wrote:
>>
>> On Thu, May 3, 2018 at 12:44 PM, Alexander Alexander
>> <[email protected]> wrote:
>> > Hi Christoph,
>> >
>> > On Wednesday, May 2, 2018 at 9:29:51 PM UTC-4, Christoph Junghans wrote:
>> >>
>> >> On Wed, May 2, 2018 at 4:37 PM, Alexander Alexander
>> >> <[email protected]> wrote:
>> >> > Thanks.
>> >> >
>> >> > On Wednesday, May 2, 2018 at 5:54:50 PM UTC-4, Christoph Junghans
>> >> > wrote:
>> >> >>
>> >> >> On Wed, May 2, 2018 at 3:37 PM, Alexander Alexander
>> >> >> <[email protected]> wrote:
>> >> >> > Hi Christoph,
>> >> >> > Thanks.
>> >> >> >
>> >> >> > On Wednesday, May 2, 2018 at 5:13:13 PM UTC-4, Christoph Junghans
>> >> >> > wrote:
>> >> >> >>
>> >> >> >> On Wed, May 2, 2018 at 1:38 PM, Alexander Alexander
>> >> >> >> <[email protected]> wrote:
>> >> >> >> > Dear all,
>> >> >> >> > I did a
>> >> >> >> > My IBI-bonded-nonbonded (after getting the nonbonded potentials
>> >> >> >> > via
>> >> >> >> > IBI-nonbonded only) crashes dues to the "...bonded interactions
>> >> >> >> > could
>> >> >> >> > not be
>> >> >> >> > calculated because some atoms
>> >> >> >> > involved moved further apart ...". By replacing the ill-bond by
>> >> >> >> > a
>> >> >> >> > harmonic
>> >> >> >> > potential in topol.top file "2 3 N 0.3453 K" where N = 1,2
>> >> >> >> > and
>> >> >> >> > K
>> >> >> >> > =
>> >> >> >> > 5000,
>> >> >> >> > the simulation are going well. Now what? what is the relation
>> >> >> >> > between
>> >> >> >> > this
>> >> >> >> > harmonic and the table_b2.xvg which was replaced by the
>> >> >> >> > harmonic
>> >> >> >> > one?
>> >> >> >> > What
>> >> >> >> > would happen for the table_b2.xvg?
>> >> >> >> Sorry, I don't understand your question! Can you rephrase?
>> >> >> >>
>> >> >> > Let's say the calculation crashes when table_b2.xvg is used but it
>> >> >> > works
>> >> >> > fine with "2 3 2 0.3453 1000" instead, then my question is
>> >> >> > that
>> >> >> > "should
>> >> >> > I continue the preregistration using "2 3 2 0.3453 1000" and
>> >> >> > forget
>> >> >> > about the table_b2.xvg? If so, what would be the final right
>> >> >> > table_b2.xvg at
>> >> >> > the end? If not so, how I can take benefit from the knowledge of
>> >> >> > "2
>> >> >> > 3
>> >> >> > 2
>> >> >> > 0.3453 1000" to improve the table_b2.xvg so that it would work as
>> >> >> > well?
>> >> >> You know generate a table with k*(r-r_0) (with r_0=0.3453 andk=1000,
>> >> >> clip out the middle part and replace it with the structured part
>> >> >> from
>> >> >> BI.
>> >>
>> >> >>
>> >> > OK, I see.
>> >> > How about this instead:
>> >> > The reason that the calculation crashes with table_b2.xvg is that the
>> >> > table_b2.xvg represents a very low K (spring constant) so that the
>> >> > two
>> >> > atoms
>> >> > are getting apart. I was reading somewhere in the mailing list that
>> >> > the
>> >> > last
>> >> > number in "2 3 8 2 1 ; 1:bond-H1-L:1" is a kind of factor for
>> >> > the
>> >> > third
>> >> > column of the table_b2.xvg, so, don't you think it would be possible
>> >> > to
>> >> > increase this factor to 2 or 3 (which means multiplying the third
>> >> > column)
>> >> > until the calculation goes fine?
>> >> Yeah, that sounds reasonable! Increasing the K helps usually helps
>> >> with the atoms getting too far apart.
>> >>
>> >> If you want to scale column 3 you will also have to modify column 2
>> >> accordingly.
>> >> Gromacs won't allow mismatching columns.
>> >
>> > I tried to scale both of the column 2 and 3 of table_b2.xvg using a lot
>> > of
>> > scale-factor, but they did not work and the missing bond ... error is
>> > still
>> > here., I guess finding the right factor is not easy.
>> > So, I tried your suggestion above, I mean k*(r-r_0) (with r_0=0.3453
>> > andk=1000. T do so, I first created a bond.pot.ib potential including 3
>> > columns as following:
>> > #-----------------
>> > bond.pot.in
>> > #column1 #column2 # column3
>> > r (1000/2)*(r-0.3453)^2 -(1000)*(r-0.3453)
>> > #-------------------
>> > And added the letter "i" to the end of each row.
Ok, I think there is some confusion about table format.
The Gromacs (xvg) table format is:
first column : Distance with unit nm
Second column : Energy with unit KJ/mol
Thirst column: Force with unit KJ/mol/nm
However the VOTCA table format is just
first column : Distance in simulation backend units
Second column : Energy in simulation backend units
Third column: flag
(see section 3.6 of the VOTCA manual)
>> > Then I tried to converted the above bond.pot.in to table_b2.xvg using
>> > "csg_call --ia-type bond --ia-name bond-H1-L --options bond-H1-L.xml
>> > convert_potential gromacs ...". But then all of the second and third
>> > columns
>> > of the new table_b2.xvg was just nan -nan.
>> > Would you please let me know if the procedure is right and where I am
>> > doing
>> > wrong?
>> Not sure, can you post your input files? (pot.in and xml)
>
> Thanks.
> Please find attached the files pot.in = Harmonic-bond-H1-L.pot.in
> The two other files are the potential associated with this bond obtained by
> normal BI crashing the calculation.
> I simply calculate the harmonic files using these two awk command:
>
> awk -v CONVFMT=%.7g '{$3 = (($1 - 0.34530000)**2)*(1000/2)} 1'
> awk -v CONVFMT=%.7g '{$4 = ($1 - 0.34530000)*(-1000)} 1'
Looking at Harmonic-bond-H1-L.pot.ib, something is screwed up.
You have duplicated r values.
$ head Harmonic-bond-H1-L.pot.ib
0.3432 0.002205 2.1
0.3432 0.002205 2.1
Something like:
$ awk 'BEGIN{for(r=0.3425;r<0.3481;r+=0.0005){print
r,((r-0.34530000)**2)*(1000/2)},"i";}' > Harmonic-bond-H1-L.pot.ib
$ csg_call --ia-type bond --ia-name bond-H1-L --options bond-H1-L.xml
convert_potential gromacs Harmonic-bond-H1-L.pot.ib table_b2.xvg
should work!
Christoph
>
> Regards,
> Alex
>
>>
>> Christoph
>> >
>> > Thank you.
>> > Alex
>> >
>> >> >>
>> >> >>
>> >> >> >
>> >> >> >>
>> >> >> >> > Figures in attachment are the plot of
>> >> >> >> > table_b2.xvg.
>> >> >> >> > I got the bonded tables including the table_b2.xvg by
>> >> >> >> > "csg_boltzmann"
>> >> >> >> > -->
>> >> >> >> > "csg_call --sloppy-tables" ---> "csg_call --ia-type bond
>> >> >> >> > --ia-name
>> >> >> >> > bond
>> >> >> >> > ...
>> >> >> >> > gromacs table_b2.xvg". And I am using the bond(angle)-*.pot.in
>> >> >> >> > as
>> >> >> >> > initial
>> >> >> >> > guesses for my IBI-all.
>> >> >> >> >
>> >> >> >> > The table_b1.xvg in gromacs manual has been defined such that
>> >> >> >> > the
>> >> >> >> > the
>> >> >> >> > r(nm),
>> >> >> >> > f(r), f'(r) are the first, second and third column of
>> >> >> >> > table_b2.xvg
>> >> >> >> > where
>> >> >> >> > f(r) is a cubic spline function in V_b(r_ij) = k*f(r_ij), If
>> >> >> >> > the
>> >> >> >> > same
>> >> >> >> > definition is applied for the table_b2.xvg obtained by the
>> >> >> >> > above
>> >> >> >> > method?
>> >> >> >> To be clear, the gromacs table format is x, f(x), -f'(x) (see
>> >> >> >> gromacs
>> >> >> >> manual 4.2.14)
>> >> >> >>
>> >> >> >> I am not sure what your question is! Gromacs uses cubic spline
>> >> >> >> internal to interpolate the table.
>> >> >> >> However, if you set cg.inverse.gromacs.table_bins in your xml
>> >> >> >> file
>> >> >> >> small enough (you had something like 0.002), then there isn't
>> >> >> >> much
>> >> >> >> to
>> >> >> >> interpolate.
>> >> >> >>
>> >> >> >>
>> >> >> >> > What is the unit of f(r)?
>> >> >> >> KJ/mol (gromacs energy units)
>> >> >> >>
>> >> >> >> > What is the unit of each column in table_b2.xvg in VOTCA?
>> >> >> >> KJ/mol/nm (gromacs force units)
>> >> >> >
>> >> >> > Just to sum up the table format, can you please confirm me that
>> >> >> > the
>> >> >> > table_b.xvg in VOTCA has the following format:
>> >> >> > first column : Distance with unit nm
>> >> >> > Second column : Energy with unit KJ/mol
>> >> >> > Thirst column: Force with unit KJ/mol/nm
>> >> >> For bonds (not angles) in gromacs that is the format!
>> >> >
>> >> > For angle the first column is degree probably.
>> >> >>
>> >> >>
>> >> >> Also for a different simulation backend, e.g. lammps this will be
>> >> >> different of course, too!
>> >> >
>> >> >
>> >> > I have one more question which your comment on would be highly
>> >> > appreciated:
>> >> > In another IBI-bonded-nonbonded parameterization the "mpirun -np 64
>> >> > gmx_mpi
>> >> > mdrun" work fine till step_021 of parameterization where it crashes
>> >> > because
>> >> > it can not find any domain decomposition for 64 ranks that is
>> >> > compatible
>> >> > with the system size. Even it works in the minimization simulation in
>> >> > step_021.
>> >> > I have already read most of the discussions about the error of domain
>> >> > decomposition, and I have tried different options like using
>> >> > different
>> >> > ranks
>> >> > (64, 32, 16, 8, 40, 36) and also -rdd ... or -dds. However, no
>> >> > success
>> >> > yet.
>> >> > I am totally confused with these parameters and I can not solve the
>> >> > issue.
>> >> > So, below I have shared the md.log files for the step_20 (which works
>> >> > fine)
>> >> > and step_21 (minimization which works fine) and step_21 (which
>> >> > crashes),
>> >> > and
>> >> > I would be so appreciated if one could help me overcome the issue.
>> >> > About the machine: Running on 4 nodes with total 64 cores, 64 logical
>> >> > cores,
>> >> > Cores per node: 16.
>> >> >
>> >> > md.log-20
>> >> > https://drive.google.com/open?id=1ZwYggDI1Hy_eYY8_nT8I50t91Wla0Obr
>> >> >
>> >> > md.log-21-mini
>> >> > https://drive.google.com/open?id=1oYE4A6fC1L8u_vx4sR8RIq3EWiG9-7YB
>> >> >
>> >> > md.log-21
>> >> > https://drive.google.com/open?id=1ff_QJrdGvLFgwGU9xMY-IcqfxzF2jkAO
>> >> Sorry, that really is a question for the gromacs user mailing list.
>> >> ([email protected])
>> >>
>> >> Christoph
>> >>
>> >> >
>> >> >
>> >> > Thank you very much.
>> >> > Regards,
>> >> > Alex
>> >> >>
>> >> >>
>> >> >> Christoph
>> >> >> >>
>> >> >> >>
>> >> >> >> >
>> >> >> >> > And would you please explain table_b2-1-3.png figure?
>> >> >> >> Not sure what there is to explain..the code on how the third
>> >> >> >> column
>> >> >> >> is
>> >> >> >> calculated is here:
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> https://github.com/votca/csg/blob/master/share/scripts/inverse/table_to_xvg.pl#L95
>> >> >> >
>> >> >> > Best regards,
>> >> >> > Alex
>> >> >> >>
>> >> >> >>
>> >> >> >> Christoph
>> >> >> >>
>> >> >> >> > Thank you very much.
>> >> >> >> > Regards,
>> >> >> >> > Alex
>> >> >> >> >
>> >> >> >> > --
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>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >> Christoph Junghans
>> >> >> >> Web: http://www.compphys.de
>> >> >> >
>> >> >> > --
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>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Christoph Junghans
>> >> >> Web: http://www.compphys.de
>> >> >
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>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
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>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
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