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? 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.
