2013/8/16 Christoph Junghans <[email protected]>: > 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). As this seems to be a frequently requested feature, I have added initial guessing from bonded target distributions via Boltzmann inversion in VOTCA 1.3-dev. So there is no need to provide a pot.in for bonded interaction in IBI anymore.
> > >> 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 -- 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.
