2013/8/14 Chandan Choudhury <[email protected]>: > > Thanks for fixing the bug. I made the changes in the source code and > re-installed votca (1.3-dev). I hope you have used "./build.sh -u" for that.
> I have executed csg_stat on two trajectories (a) coarse-grained atomistic > trajectory and (b) trajectory after step_001 with the following commands: > > (a) csg_stat --cg > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/pc_new_cg.xml > --options > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/settings_bon_nb.xml > --nt 8 --trj cg_traj.trr --top > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/step_001/topol.tpr > > I obtain well behaved distribitions for each of the bonds. > > (b) csg_stat --cg > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/pc_new_cg.xml > --options > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/settings_bon_nb.xml > --nt 8 --trj ../traj.xtc --top > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/step_001/topol.tpr > > But for the step_001 trajectory, distributions for AB and DB are wiered. In > this trajectory the g_rdf and csg_boltzmann command works very fine. That seems really strange, because VOTCA only read the positions from the xtc file. All the topological information comes out of the tpr file. Hence the mapping and settings file seem to be correct. But double-check that the beads from the AB and DB bond appear in $ csg_dump --top topol.tpr Does your confout.gro from step_001 contain NaNs ? Do you get valid distributions if you are using conf.gro or confout.gro instead of traj.xtc? Christoph > > I have no clue what wrong I am doing. > > Because of the wiered behaviour of AB.bond.dist.new. I am getting following > error: > ***************************************************** > working directory: > /data/home/chandan/Documents/votca/polycarbonate/trimer/new_mapping/re/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.Ypjxs > AB.bond.dist.tgt_extrapolated.JWxob' (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.JWxob > 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/re/inverse.log > # > # > # > ########################################################################################################################################################################### > ***************************************************** > > Kindly suggest how to overcome this. > > Chandan > > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > On Wed, Aug 14, 2013 at 10:49 AM, Chandan Choudhury <[email protected]> > wrote: >> >> Dear Christoph, >> >> Thanks for fixing the bug. I made the changes in the source code and >> re-installed votca (1.3-dev). >> >> The thing which has been troubling very much is the bonded distributions >> of AB and DB. The sequence of the polymer is A-B1-C1-D1-B2-C2-D2-B3-E. The >> other distributions (BC, CD and BE) shows the same behaviour as from the >> g_rdf (nrexcl=0) command. Infact, on using the csg_boltzmann on the >> trajectory of step_001, I obtain a well behaved distributions fo all the >> bond distributions. Infact plots are overlapping for BC, CD and BE (when >> compared with csg_stat). >> I donot understand why only these to bonds are behaving in a different >> way. I have attached the output of AB and DB bonds. AB contains -nan-. >> >> One way to get rid of it, I suppose would be to use csg_boltzmann tool. >> Can it be used for bonded part? >> >> Chandan >> >> >> >> -- >> Chandan kumar Choudhury >> NCL, Pune >> INDIA >> >> >> On Wed, Aug 14, 2013 at 3:34 AM, Christoph Junghans <[email protected]> >> wrote: >>> >>> 2013/8/13 Christoph Junghans <[email protected]>: >>> > 2013/8/13 Chandan Choudhury <[email protected]>: >>> >> >>> >> Dear users, >>> >> >>> >> I am using votca version 1.3-dev for cg simulation. >>> >> At step_001, after the simulation by gromacs, csg_stat runs and it >>> >> computes >>> >> the distributions (reads the setting.xml and mapping_cg.xml). >>> >> >>> >> My system and 5 different beads with 5 bond and 5 angles. >>> >> >>> >> While surprisingly, csg_stat produces incorrect distributions for the >>> >> AB.bond and DB.bond (xvg attached). >>> >> As a cross check, I executed the same csg_stat command on the cg >>> >> trajectory, >>> >> which was generated from atomistic simulations (with same setting amd >>> >> mapping files). The command executes and the plots are reasonable. >>> >> So, the mapping and setting files are correct. >>> >> >>> >> Also, I have used the g_rdf (with exclusion 0), to compute the bond >>> >> distributions. The distributions for BC, CD and BE matches while for >>> >> AB and >>> >> DB bonds, it didnot match. I cannot undestand where I am mistaken. >>> >> Kindly >>> >> suggest me. >>> > The bonded ibi feature in new in votca 1.3, it might not be very well >>> > tested. >>> > >>> > I have the suspicion that the normalization for the bonded interaction >>> > might be inconsistent in csg_stat. >>> > Usually that has no effect on IBI as the only thing, which matters is >>> > the ratio, so it will works as long as the target distribution has the >>> > same normalization. >>> > >>> > I will have a look into it soon. >>> Actually, there was a bug! I fixed it: >>> >>> <https://code.google.com/p/votca/source/detail?r=ea8e40fb78693ba6fe2dd1d544aff6d6e111b845&repo=csg> >>> and also updated the tutorials: >>> >>> <https://code.google.com/p/votca/source/detail?r=6e0f1991ad31eda3a86e660637f156a514f217a1&repo=csg-tutorials> >>> >>> I didn't added the factor 1/r , 1/sin at this point, but for IBI that >>> didn't matter much as long as the target distribution is generated >>> with csg_stat, too. >>> >>> Christoph >>> > >>> > For all the other readers, bonded distribution in csg_boltzmann are >>> > correct and non-bonded distribution in csg_stat, too. The thing in >>> > question are bonded distribution from csg_stat! >>> > >>> >> >>> >> N.B: I have also attached the settings and mapping files. >>> >> -- >>> >> 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 >>> >>> >>> >>> -- >>> 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. 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