On Thursday, May 3, 2018 at 4:56:25 PM UTC-4, Christoph Junghans wrote:
>
> On Thu, May 3, 2018 at 1:46 PM, Alex <[email protected] <javascript:>>
> wrote:
> >
> > On Thu, May 3, 2018 at 3:03 PM, Christoph Junghans <[email protected]
> <javascript:>>
> > wrote:
> >>
> >> On Thu, May 3, 2018 at 12:44 PM, Alexander Alexander
> >> <[email protected] <javascript:>> 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)
>
Probably you mena the *.pot.ib or *.pot.in we get from csg_boltzmann.
Otherwise after converting them to the gromacs format by by csg_call... ..
convert_potential gromacs... they have the gromacs units and formats.
>
> >> > 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!
>
Wow, it works now, thank you.
Just one issue; in "2 3 2 0.3453 K" of harmonic potential , different K
from 500 to 50000 could work in this system, and then each K would give
different pot.ib and table_b2.xvg of course with
(r-0.34530000)**2)*(1000/2), so, which one (K) is good to choose?
One more question:
After a IBI-nonbonded for a system, I am doing now IBI-bonded-nonbonded for
that system which has two bond types and one angle. They started with a
promising fit with their dist.tgt's but afterward they do not have any
sensible improvement after 115 step now, even the angle.dist.new is loosing
gradually its agreement with angle.dist.tgt. I was wondering what might be
the reason? Below is part of my settings.xml file: The <scale>1.5</scale>
in the first bond I choose just because I though it might help improvement,
but no considerable improvement.
<name>bond-D-E</name>
<min>0.200</min>
<max>0.500</max>
<step>0.0005</step>
<inverse>
<target>bond-D-E.dist.tgt</target>
<do_potential>1 0 0</do_potential>
<post_update>smooth</post_update>
<post_update_options>
<scale>1.5</scale>
</post_update_options>
<post_add>convergence</post_add>
<gromacs>
<table>table_b1.xvg</table>
</gromacs>
</inverse>
</bonded>
<!-- %%% -->
<bonded>
<name>angle-D-E-F</name>
<min>2.0</min>
<max>3.0</max>
<step>0.001</step>
<inverse>
<target>angle-D-E-F.dist.tgt</target>
<do_potential>0 0 1</do_potential>
<post_update>smooth</post_update>
<post_update_options>
<scale>0.1</scale>
</post_update_options>
<post_add>convergence</post_add>
<gromacs>
<table>table_a1.xvg</table>
</gromacs>
</inverse>
</bonded>
Thank you.
Regards,
Alex
>
> 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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> >> >> >> >> > 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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> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> 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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