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. 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