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...
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. 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