On Wed, Aug 14, 2013 at 10:08 PM, Christoph Junghans <[email protected]>wrote:
> 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 are very right. My min and max were too narrow for them. Now, it does work. Thanks once again. > > 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. > > > -- You received this message because you are subscribed to the Google Groups "votca" group. 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