potential_shift.pl error in VOTCA for bonded potentials
87 views
Skip to first unread message
Satyen Dhamankar
Sep 2, 2021, 11:21:05 AM9/2/21
to votca
Hello,
I am running a linear 40mer-ibi simulation, with the end beads being of Type TA and TB, and everything in between is a bead of type TM, immersed in water (single bead, TW).
I am running IBI on it, by considering the rdfs TW-TW, TW-TA, TW-TB, TW-TM, and bonded distributions between TA-TM, TM-TM, and TM-TB. I obtained the non-bonded distributions using csg_stat, and the bonded distribution using csg_boltzmann.
This is the error I am getting after I run my csg_inverse script:
step 0 done
^[[34;01mDoing iteration 1 (dir step_001)^[[0m
Simulation with gromacs
^[[34;01mAutomatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated interactions only work with Group cutoff-scheme!^[[0m
^[[34;01mAutomatically added '-tableb table_b1.xvg table_b2.xvg table_b3.xvg to mdrun options (add -tableb option to cg.inverse.gromacs.mdrun.opts yourself if this is wrong)^[[0m
Make update for ibi
Calculating rdfs with csg_stat using 28 tasks
Doing post-update for ibi
Adding up potential
Post add
Postadd tasks for TW-TW: convergence
Postadd tasks for TW-TTA: convergence
Postadd tasks for TW-TTB: convergence
Postadd tasks for TW-TM: convergence
step 1 done, needed 11638 secs
Doing convergence check: default
Iterations are not converged, going on
^[[34;01mDoing iteration 2 (dir step_002)^[[0m
Simulation with gromacs
^[[34;01mAutomatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated interactions only work with Group cutoff-scheme!^[[0m
^[[34;01mAutomatically added '-tableb table_b1.xvg table_b2.xvg table_b3.xvg to mdrun options (add -tableb option to cg.inverse.gromacs.mdrun.opts yourself if this is wrong)^[[0m
Make update for ibi
Calculating rdfs with csg_stat using 28 tasks
^[[31;01m######################################################################################################################################################################################################################
# #
# ERROR: #
# do_external: subscript #
# /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/potential_shift.pl --type bond BOTA.dpot.pure_ibi BOTA.dpot.new #
# (from tags potential shift) failed #
# For details see the logfile /tigress/satyend/pnipam_tigergpu/PNIPAM_SIMS/UNIQUE_INITIAL_CONFIG/40NIPAM/7x7x7/330K-proc2/CG/FortyBead/ibi_bonds/inverse.log #
# #
######################################################################################################################################################################################################################^[[0m
I am not adept at reading Perl scripts, and I wanted to ask, what is the reason, and nature of such an error? How do I go about debugging this?
Satyen Dhamankar
Sep 2, 2021, 11:21:45 AM9/2/21
to votca
Furthermore, why did I not receive this error in the first iteration?
Christoph Junghans
Sep 2, 2021, 11:59:34 AM9/2/21
to vo...@googlegroups.com
On Thu, Sep 2, 2021 at 9:21 AM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> Furthermore, why did I not receive this error in the first iteration?
Look at your inverse.log for details. But my guess is that the
>
> Furthermore, why did I not receive this error in the first iteration?
potential has no valid point in it.
Have a look at the BOTA.dpot.pure_ibi file in the last step directory.
I would try to pick the min and max of said bonded interaction a bit more tight.
Christoph
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
> 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 view this discussion on the web visit https://groups.google.com/d/msgid/votca/828b9a44-0704-446a-bb9b-5c6f86574556n%40googlegroups.com.
--
Christoph Junghans
Web: http://www.compphys.de
Satyen Dhamankar
Sep 3, 2021, 11:58:53 AM9/3/21
to votca
Hi Christoph,
Yes, it seem like BOTA.dpot.pure_ibi is just a collection of zeros.
the BOTA.dist.tgt file goes from 0.360024 to 0.673874, in steps of approximately 0.00313.
In settings.xml for <bonded> interactions, I have put min as 0.37, max as 0.67 and step as 0.001.
My question is, should my min, max and step size be exactly the same as the target distribution?
Christoph Junghans
Sep 3, 2021, 12:02:04 PM9/3/21
to vo...@googlegroups.com
On Fri, Sep 3, 2021 at 9:58 AM Satyen Dhamankar <saty...@gmail.com> wrote:
>
> Hi Christoph,
> Yes, it seem like BOTA.dpot.pure_ibi is just a collection of zeros.
> the BOTA.dist.tgt file goes from 0.360024 to 0.673874, in steps of approximately 0.00313.
> In settings.xml for <bonded> interactions, I have put min as 0.37, max as 0.67 and step as 0.001.
>
> My question is, should my min, max and step size be exactly the same as the target distribution?
you need to leave some space on the left and the right so the
>
> Hi Christoph,
> Yes, it seem like BOTA.dpot.pure_ibi is just a collection of zeros.
> the BOTA.dist.tgt file goes from 0.360024 to 0.673874, in steps of approximately 0.00313.
> In settings.xml for <bonded> interactions, I have put min as 0.37, max as 0.67 and step as 0.001.
>
> My question is, should my min, max and step size be exactly the same as the target distribution?
interpolation can be done correctly.
I would pick the min at the point where the target distribution is >0
and then add another 5 bins to it.
Same for the max, but subtracting 5 bins.
Satyen Dhamankar
Sep 4, 2021, 12:24:37 AM9/4/21
to votca
Hi Christoph,
I tried what you suggested, wherein I deleted step_002 folder, put in the new limits of my bonded interaction BOTA, as mentioned above.
This is what I see in my inverse.log file:
Running subscript 'update_ibi_pot.pl BOTA.dist.tgt BOTA.dist.new BOTA.pot.cur BOTA.dpot.pure_ibi 2.7437883' (from tags update ibi_pot) dir /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
Running subscript 'potential_shift.pl --type bond BOTA.dpot.pure_ibi BOTA.dpot.new' (from tags potential shift) dir /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
No valid value found in BOTA.dpot.pure_ibi at /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/potential_shift.pl line 87.
Callstack:
/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/inverse.sh - linenumber 266
do_external - linenumber 177 in /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/functions_common.sh /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/update_ibi.sh - linenumber 32
for_all - linenumber 22 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat function do_external')
/home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/update_ibi_single.sh - linenumber 42
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/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse/potential_shift.pl --type bond BOTA.dpot.pure_ibi BOTA.dpot.new #
# (from tags potential shift) failed
However, right above this message, I also see this:
Does this seem to still be a problem with the limits of the interpolation?
Running critical command 'mktemp BOTA.dist.tgt_extrapolated.XXXXX'
Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 --region leftright BOTA.dist.tgt_smooth.iw2Xo BOTA.dist.tgt_extrapolated.c9OL9' (from tags table extrapolate) dir /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
table_extrapolate.pl: extrapolating the left using linear with gradient 0
table_extrapolate.pl: extrapolating the right using linear with gradient -412.836555929354
Running subscript 'dist_adjust.pl BOTA.dist.tgt_extrapolated.c9OL9 BOTA.dist.tgt' (from tags dist adjust) dir /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
Does this seem to still be a problem with the limits of the interpolation?
Christoph Junghans
Sep 4, 2021, 12:19:00 PM9/4/21
to vo...@googlegroups.com
> I tried what you suggested, wherein I deleted step_002 folder, put in the new limits of my bonded interaction BOTA, as mentioned above.
If you change min and max you might have to redo everything, incl.
step_000 and step_001
>
> This is what I see in my inverse.log file:
>
> Running subscript 'update_ibi_pot.pl BOTA.dist.tgt BOTA.dist.new BOTA.pot.cur BOTA.dpot.pure_ibi 2.7437883' (from tags update ibi_pot) dir /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
Another way to understand this is to run "update_ibi_pot.pl" with
> This is what I see in my inverse.log file:
>
> Running subscript 'update_ibi_pot.pl BOTA.dist.tgt BOTA.dist.new BOTA.pot.cur BOTA.dpot.pure_ibi 2.7437883' (from tags update ibi_pot) dir /home/satyend/software/spack/opt/spack/linux-rhel7-broadwell/gcc-9.3.1/votca-csg-2021-vh2kxfbymvudsn3en3wk5xxnie4j73nq/share/votca/scripts/inverse
options "BOTA.dist.tgt BOTA.dist.new BOTA.pot.cur BOTA.dpot.pure_ibi
2.7437883'" by hand to understand why the result is all zeros.
Christoph
Satyen Dhamankar
Sep 5, 2021, 3:49:25 PM9/5/21
to votca
Hi Christoph,
I am running update_ibi_pot.pl on BOTA.dist.tgt, BOTA.dist.new, and BOTA.pot.cur. I see that BOTA.dpot.pure_ibi is still zeros.
However, I also see that BOTA.dist.new is also a file full of zeros. Does this mean that my bond-distribution for my simulation is being calculated incorrectly?
Christoph Junghans
Sep 5, 2021, 6:40:08 PM9/5/21
to vo...@googlegroups.com
> I am running update_ibi_pot.pl on BOTA.dist.tgt, BOTA.dist.new, and BOTA.pot.cur. I see that BOTA.dpot.pure_ibi is still zeros.
>
> However, I also see that BOTA.dist.new is also a file full of zeros. Does this mean that my bond-distribution for my simulation is being calculated incorrectly?
That is a good catch.
>
> However, I also see that BOTA.dist.new is also a file full of zeros. Does this mean that my bond-distribution for my simulation is being calculated incorrectly?
You can just run that last csg_stat command from inverse.log ("grep
csg_stat inverse.log") to see if you can reproduce the empty
distributions.
Is this an angle? (Remember VOTCA calculates angles in radian).
Otherwise you might need to check your 1:1 mapping file again.
("csg_dump --top .. --cg" can be of help")
Christoph
Satyen Dhamankar
Sep 5, 2021, 11:18:08 PM9/5/21
to votca
Hi Christoph,
Yes, I did run csg_stat on my distributions. Seems like there is something wrong about it as I did get the zeros, again.
I did try csg_dump --top topol.tpr --cg fortynipam_cg.xml, and I got mappings that looked sound...
Christoph Junghans
Sep 6, 2021, 11:24:49 AM9/6/21
to vo...@googlegroups.com
> Yes, I did run csg_stat on my distributions. Seems like there is something wrong about it as I did get the zeros, again.
Can you open an issue on https://github.com/votca/csg/issues, include
all the input files for the csg_stat call and we will have a look?
Christoph
Satyen Dhamankar
Sep 6, 2021, 12:27:46 PM9/6/21
to votca
Hi Christoph,
I have opened an issue on github. Please let me know if you need any more information.
Christoph Junghans
Sep 6, 2021, 1:04:49 PM9/6/21
to vo...@googlegroups.com
> I have opened an issue on github. Please let me know if you need any more information.
I had a quick look, and it seems you pick the max too small (at least
for the BOTA bond), please discuss the details on the issue.
Christoph
Christoph Junghans
Sep 6, 2021, 1:16:20 PM9/6/21
to vo...@googlegroups.com
On Mon, Sep 6, 2021 at 11:04 AM Christoph Junghans <jung...@votca.org> wrote:
>
> On Mon, Sep 6, 2021 at 10:27 AM Satyen Dhamankar <saty...@gmail.com> wrote:
> >
> > Hi Christoph,
> >
> > I have opened an issue on github. Please let me know if you need any more information.
> I had a quick look, and it seems you pick the max too small (at least
> for the BOTA bond), please discuss the details on the issue.
FYI, for the others see here: https://github.com/votca/csg/issues/709
>
> On Mon, Sep 6, 2021 at 10:27 AM Satyen Dhamankar <saty...@gmail.com> wrote:
> >
> > Hi Christoph,
> >
> > I have opened an issue on github. Please let me know if you need any more information.
> I had a quick look, and it seems you pick the max too small (at least
> for the BOTA bond), please discuss the details on the issue.
Reply all
Reply to author
Forward
0 new messages