On Mon, Sep 6, 2021 at 11:04 AM Christoph Junghans <[email protected]> wrote: > > On Mon, Sep 6, 2021 at 10:27 AM Satyen Dhamankar <[email protected]> wrote: > > > > Hi Christoph, > > > > I have opened an issue on github. Please let me know if you need any more > > information. > I had a quick look, and it seems you pick the max too small (at least > for the BOTA bond), please discuss the details on the issue. FYI, for the others see here: https://github.com/votca/csg/issues/709 > > Christoph > > > On Monday, September 6, 2021 at 11:24:49 AM UTC-4 Christoph Junghans wrote: > >> > >> On Sun, Sep 5, 2021 at 9:18 PM Satyen Dhamankar <[email protected]> wrote: > >> > > >> > 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. > >> Can you open an issue on https://github.com/votca/csg/issues, include > >> all the input files for the csg_stat call and we will have a look? > >> > >> Christoph > >> > >> > 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. > >> > 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/0ed5de6b-b227-4fbe-b388-702f68a174cdn%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/0e4c4c53-b560-456e-909f-4b001a3b2c11n%40googlegroups.com. > > > > -- > Christoph Junghans > Web: http://www.compphys.de
-- 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/CAHG27e4gshp_tt1DGOTjNs4e0cJa9oOsiQ-nzw%3D83AqKSmB%2Buw%40mail.gmail.com.
