On Thu, Mar 15, 2018 at 10:08 AM, Amy Rice <[email protected]> wrote: > I took a closer look at update_ibi_pot.pl and it seems this lack of overlap > is definitely the issue, since the script only calculates dU in regions > where both distributions are non-zero: > > --------------------update_ibi_pot.pl, lines 70-72------------------- > > if (($rdf_aim[$i] > 1e-10) && ($rdf_cur[$i] > 1e-10)) { > > $dpot[$i]=log($rdf_cur[$i]/$rdf_aim[$i])*$pref; > > $flag[$i]="i"; > > ---------------------------------------------------------------------------- > > > Are there any suggestions on ways to work around this? One though I had was > to edit this script to check first for overlap, and if non exists, then set > $rdf_aim[$i]= 1e-9. This would allow dU to be calculated in the region where > rdf_cur is non-zero and would solve the problem of having the dU output file > containing only zeros. I am not familiar/experienced enough with IBI to know > if this would be a reasonable work around though. Any suggestions or advice > would be greatly appreciated! Well, the potential update is difference of the potentials of mean force (something like U_pmf_cur-U_pmf_target), so if either of the distributions is 0, log (rdf=0) would be minus infinity, which doesn't make much sense. For that reason, we don't calculate the update there and flag it as invalid ("i").
Back to solving your problem, you could either pick the minimum of the interaction (min property) bigger than 0, so that the target rdf is bigger than 0 as well. Or you could use a well-constrained initial guess for the potential (<NAME>.pot.in file) and update that slowly. Both directions have been discussed on the mailing list in the past, have a search on the web forum. Christoph > Thank you again, > - Amy > > > > On Wednesday, March 14, 2018 at 6:02:12 PM UTC-5, Amy Rice wrote: >> >> Hi all, >> >> I am trying to use IBI to refine one of the bonded potentials in my CG >> system. The initial guess and step_001 gromacs simulation run without issue, >> but it fails to update the potential at this step. The detailed error output >> from inverse.log is pasted below. It seems to me that the issue isn't with >> the potential_shift.pl step, which (I think) just fails because >> SNa-SC2.dpot.pure_ibi has no non-zero values in it; I think the problem >> arises during the "update_ibi_pot" step when dU is calculated. I noticed >> that the current rdf is quite far from the target distribution and wonder if >> this could be causing some problems? I've attached the two distributions, >> the current potential and pure_ibi files, and the full log file. Please let >> me know if there is any other information I can provide that will be of help >> troubleshooting this problem. >> >> ------------------------------------from >> inverse.log--------------------------------------------------------------- >> >> Running critical command 'mktemp SNa-SC2.dist.tgt_extrapolated.XXXXX' >> Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 >> --region leftright SNa-SC2.dist.tgt_smooth.PP6mM >> SNa-SC2.dist.tgt_extrapolated.w36Sf' (from tags table extrapolate) dir >> /home/arice3/Programs/votca/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 0 >> Running subscript 'dist_adjust.pl SNa-SC2.dist.tgt_extrapolated.w36Sf >> SNa-SC2.dist.tgt' (from tags dist adjust) dir >> /home/arice3/Programs/votca/share/votca/scripts/inverse >> Running subscript 'update_ibi_pot.pl SNa-SC2.dist.tgt SNa-SC2.dist.new >> SNa-SC2.pot.cur SNa-SC2.dpot.pure_ibi 2.49435' (from tags update ibi_pot) >> dir /home/arice3/Programs/votca/share/votca/scripts/inverse >> Running subscript 'potential_shift.pl --type bond SNa-SC2.dpot.pure_ibi >> SNa-SC2.dpot.new' (from tags potential shift) dir >> /home/arice3/Programs/votca/share/votca/scripts/inverse >> No valid value found in SNa-SC2.dpot.pure_ibi at >> /home/arice3/Programs/votca/share/votca/scripts/inverse/potential_shift.pl >> line 87. >> >> Callstack: >> /home/arice3/Programs/votca/share/votca/scripts/inverse/inverse.sh - >> linenumber 264 >> do_external - linenumber 176 in >> /home/arice3/Programs/votca/share/votca/scripts/inverse/functions_common.sh >> >> /home/arice3/Programs/votca/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/arice3/Programs/votca/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/arice3/Programs/votca/share/votca/scripts/inverse/potential_shift.pl >> --type bond SNa-SC2.dpot.pure_ibi SNa-SC2.dpot.new # >> # (from tags potential shift) failed >> # >> # For details see the logfile /local/VOTCA/IBI_test/inverse.log >> # >> # >> # >> >> ################################################################################################################################# >> die: (called from 16487) CSG_MASTER_PID is 12694 >> die: pids to kill: 12694 15891 16472 16487 >> >> >> ----------------------------------------------------------------------------------------------------------------------------------------------- >> >> Thank you for the help, >> - Amy >> > -- > 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 post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- Christoph Junghans Web: http://www.compphys.de -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
