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/CAHG27e6e9s%3D2xHkpFWsgpLyMREO4Xz2yEfGHfzvVujT6evfNEw%40mail.gmail.com.
