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/CAHG27e4rT_mHbSXOnkZ3hLt%3D%3D3891QJgD6vfi0%2B0fac6yCO1TA%40mail.gmail.com.
