On Sun, Sep 5, 2021 at 9:18 PM Satyen Dhamankar <[email protected]> wrote: > > 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. 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 > I did try csg_dump --top topol.tpr --cg fortynipam_cg.xml, and I got mappings > that looked sound... > > On Sunday, September 5, 2021 at 6:40:08 PM UTC-4 Christoph Junghans wrote: >> >> On Sun, Sep 5, 2021 at 1:49 PM Satyen Dhamankar <[email protected]> wrote: >> > >> > 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? >> That is a good catch. >> 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 >> > >> > On Saturday, September 4, 2021 at 12:19:00 PM UTC-4 Christoph Junghans >> > wrote: >> >> >> >> On Fri, Sep 3, 2021 at 10:24 PM Satyen Dhamankar <[email protected]> >> >> wrote: >> >> > >> >> > 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. >> >> 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 >> >> 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 >> >> >> >> > 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: >> >> > >> >> > 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? >> >> > On Friday, September 3, 2021 at 12:02:04 PM UTC-4 Christoph Junghans >> >> > wrote: >> >> >> >> >> >> On Fri, Sep 3, 2021 at 9:58 AM Satyen Dhamankar <[email protected]> >> >> >> 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 >> >> >> 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. >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > >> >> >> > On Thursday, September 2, 2021 at 11:59:34 AM UTC-4 Christoph >> >> >> > Junghans wrote: >> >> >> >> >> >> >> >> On Thu, Sep 2, 2021 at 9:21 AM Satyen Dhamankar <[email protected]> >> >> >> >> 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 >> >> >> >> 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 >> >> >> >> >> >> >> >> > >> >> >> >> > On Thursday, September 2, 2021 at 11:21:05 AM UTC-4 Satyen >> >> >> >> > Dhamankar wrote: >> >> >> >> >> >> >> >> >> >> 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? >> >> >> >> > >> >> >> >> > -- >> >> >> >> > 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 [email protected]. >> >> >> >> > 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 >> >> >> > >> >> >> > -- >> >> >> > 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 [email protected]. >> >> >> > To view this discussion on the web visit >> >> >> > https://groups.google.com/d/msgid/votca/252a1715-e19c-40fd-983f-5db77b7e5db7n%40googlegroups.com. >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Christoph Junghans >> >> >> Web: http://www.compphys.de >> >> > >> >> > -- >> >> > 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 [email protected]. >> >> > To view this discussion on the web visit >> >> > https://groups.google.com/d/msgid/votca/6e344da6-b41e-4b0a-ac0e-d74713b188c6n%40googlegroups.com. >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > 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 [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/fdf9c63e-9bf9-45ec-9e09-747975d744edn%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > 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 [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/0ed5de6b-b227-4fbe-b388-702f68a174cdn%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e6k0n1x-6-MVN%3DL374sUviwGTg%3DrXgOgk74ZwXjLzaBDA%40mail.gmail.com.
