2013/8/15 Chandan Choudhury <[email protected]>: > > On Thu, Aug 15, 2013 at 10:48 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2013/8/15 Chandan Choudhury <[email protected]>: >> > Dear votca users, >> > >> > The atomisitc trajectory produces a distribution of AB bond in the >> > range >> > from 0.44 to 0.45 nm. While the potential (input) is also generated. >> > This >> > distribution and potential are generated using csg_stat and latter from >> > both >> > the plots, the bad sampled regions are removed. Kepping the range same. >> > >> > Now, when I procede for iteration at step_001. The peak positon for AB >> > bond >> > is off and the range is from 0.34 to 0.40. My final aim is to converge >> > both >> > the distributions. Thus using IBI. >> > >> > Now problem what I encounter, is that if the min and max in the >> > cg.bonded >> > is kept according to the atomistic distribution, then I miss out the >> > distribution in the iteration step (steep_001). >> > When I decrease the min to 0.30 and increase the max to 0.54, I do find >> > the >> > AB distribution in step_001. But after that the following error is >> > encountered: >> > >> > >> > working directory: >> > >> > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/iterate_bond/step_001' >> > Running critical command 'mktemp AB.bond.dist.tgt_extrapolated.XXXXX' >> > Running subscript 'table_extrapolate.pl --function linear --avgpoints 1 >> > --region leftright AB.bond.dist.tgt_smooth.OYNVr >> > AB.bond.dist.tgt_extrapolated.4g5KN' (from tags table extrapolate) dir >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse >> > Running subscript 'dist_adjust.pl AB.bond.dist.tgt_extrapolated.4g5KN >> > AB.bond.dist.tgt' (from tags dist adjust) dir >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse >> > Running subscript 'update_ibi_pot.pl AB.bond.dist.tgt AB.bond.dist.new >> > AB.bond.pot.cur AB.bond.dpot.pure_ibi' (from tags update ibi_pot) dir >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse >> > Running critical command 'sed -n s/.*cg_bonded\.\([^[:space:]]*\) >> > .*/\1/p' >> > Running subscript 'dpot_shift_bo.pl AB.bond.dpot.pure_ibi >> > AB.bond.dpot.new' >> > (from tags dpot shift_bonded) dir >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse >> > No valid value found in AB.bond.dpot.pure_ibi at >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/dpot_shift_bo.pl >> > line >> > 51. >> > >> > Callstack: >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/inverse.sh - >> > linenumber >> > 265 >> > do_external - linenumber 171 in >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/functions_common.sh >> > >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/update_ibi.sh - >> > linenumber 32 >> > for_all - linenumber 17 (see 'csg_call --cat function >> > for_all') >> > do_external - linenumber 19 (see 'csg_call --cat >> > function do_external') >> > >> > /opt/apps/votca/1.3-dev/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 >> > /opt/apps/votca/1.3-dev/share/votca/scripts/inverse/dpot_shift_bo.pl >> > AB.bond.dpot.pure_ibi AB.bond.dpot.new (from tags dpot shift_bonded) >> > failed >> > # >> > # For details see the logfile >> > >> > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/iterate_bond/inverse.log >> > # >> > # >> > # >> > >> > ########################################################################################################################################################################### >> > >> > >> > The AB.bond.dpot.pure_ibi contains 0 for all the values between 0.3 to >> > 0.54. >> > Can anyone guide me regarding this? >> Strange! >> >> Can you send me AB.bond.dist.tgt AB.bond.dist.new AB.bond.pot.cur from >> that step? >> > Dear Christoph, > > Thanks for looking at it. Please find in the files in the attachment. Ok, I got it!
Your distribution don't overlap, then no IBI update can be calculated. log (x/y) is only valid, if x and y are bigger 0. I am guessing your initial potential is too weak, try to make it steeper around 0.44 to 0.45 nm. Christoph > > Chandan >> >> Christoph >> > >> > -- >> > Chandan kumar Choudhury >> > NCL, Pune >> > INDIA >> > >> > -- >> > 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 http://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/groups/opt_out. >> >> >> >> -- >> 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 http://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/groups/opt_out. > > > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
