Thank you for this. Need a bit more reading then :) Steven
W dniu piątek, 16 sierpnia 2013 17:09:19 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/8/16 <[email protected] <javascript:>>: > > 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.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]. > >> >> > 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] <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]. 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.
