2013/8/14 Chandan Choudhury <[email protected]>: > > On Wed, Aug 14, 2013 at 7:39 PM, Christoph Junghans <[email protected]> > wrote: >> >> 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 re-downloaded and compiled tools and csg . see: <https://code.google.com/p/votca/wiki/Installing#Update> >> >> >> > 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 > > > Please have a look at the attachment. Looks ok!
>> >> >> Does your confout.gro from step_001 contain NaNs ? > > No. Neither conf.pdb or confout.pdb contains NaNs. >> >> Do you get valid distributions if you are using conf.gro or >> confout.gro instead of traj.xtc? > > I obtain NaNs on for AB and BD bonds. Well, I understand that. Before the distribution as empty, hence its norm_1 is 0 and when normalizing -> 0/0=NaN Maybe you made min and max to narrow for the AB and BD bond, so that no values fall in there. You could use g_dist on cg trajectory or make min=0 and max=10000 to check that. >> >> >> 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. >> 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.
