2013/8/16 <[email protected]>: > 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? There is no initial guesses for the distributions! There are initial potentials and target distributions don't mix them up.
Bonded IBI only working VOTCA 1.3-dev and as you can see from the other thread on the mailing list, it is still experimental. The iteration is done using csg_inverse with an additional mapping file. At this point, VOTCA needs a target distributions with the normalization like csg_stat produces it. (So no 1/r or 1/sin factor, but the integral normalized to 1, this is subject to future changes.) Additionally VOTCA needs an initial potential (log(distribution)+ extrapolation). > Steven > > W dniu piątek, 16 sierpnia 2013 01:21:55 UTC+1 użytkownik Christoph Junghans > napisał: >> >> 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. -- 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.
