I also have a question regarding bonded parameters using IBI. The initial guess of those distributions should be an outcome from g_angle -dihedral -dist or csg_boltzmann? They do differ quite significantly. Which tool VOTCa uses during the iteration of dihedrals?
Steven W dniu piątek, 16 sierpnia 2013 01:21:55 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/8/15 Chandan Choudhury <[email protected] <javascript:>>: > > > > On Thu, Aug 15, 2013 at 10:48 PM, Christoph Junghans > > <[email protected]<javascript:>> > > > wrote: > >> > >> 2013/8/15 Chandan Choudhury <[email protected] <javascript:>>: > >> > 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.plAB.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] <javascript:>. > >> > To post to this group, send email to > >> > [email protected]<javascript:>. > > >> > 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] <javascript:>. > >> To post to this group, send email to [email protected]<javascript:>. > > >> 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] <javascript:>. > > To post to this group, send email to [email protected]<javascript:>. > > > 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. 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