2013/10/1 Chandan Choudhury <[email protected]>: > On Tue, Oct 1, 2013 at 2:13 AM, Christoph Junghans <[email protected]> > wrote: >> >> >> The trajectory is missing, just send a conf.gro. One frame will be >> enough to check for the error. > > > I have attached conf.gro >> >> >> These are two separate issues. >> >> 1.) The difference between g_rdf and csg_stat without mapping file >> Could you check that all exclusion you expect, show up in: >> $ csg_stat --top topol.tpr --execl >> and compare to the exclusion in >> $ gmxdump -s topol.tpr > > > csg_dump --excl --top ../topol.tpr > excl_csg > csg_dump --excl --top ../topol.tpr --cg pc_new_cg.xml > excl_csg_pc > > The exclusion list for csg_dump with and without pc_new_cg.xml are same. I > could not clearly understand the exclusions of the gromacs. > > I have attached the output of the csg_dump and gmxdump. > >> 2.) The difference between csg_stat with and without mapping file >> For this you have to understand how exclusion in VOTCA. >> If you don't specify a mapping file, exclusion are just read for the >> topology (tpr). >> If you specify a mapping file, exclusion are generated by VOTCA due to >> the following rule. >> Everything which is connected via a bond, angle or dihedral is excluded. >> In your case to generate exclusion equivalent to nrexcl=3, you will >> need add some extra dihedrals to the mapping file (with evaluating >> them). >> >> If you are unsure compare: >> $ csg_stat --top topol.tpr --execl >> with >> $ csg_stat --top topol.tpr --execl --cg pc_new_cg.xml > > > I could understand that. Thanks for pointing out. On supplying the > pc_new_cg.xml to csg_dump the excl matches. > > When I execute : > csg_stat --nt 8 --options settings.xml --top ../topol.tpr --trj ../traj.xtc > --begin 20 --first-frame 0 --cg pc_new_cg.xml > I obtain only the B-D.dist.new (as the settings.xml contains the information > about the B-D.) > > When I perform : > csg_stat --nt 8 --options settings_all.xml --top ../topol.tpr --trj > ../traj.xtc --begin 20 --first-frame 0 --cg pc_new_cg.xml > > I obtain all the bonded and non-bonded distributions. B-D.dist_all.new. > In both the cases the pc_new_cg has been updated with the inclusion of > dihedral information. > > It can be seen that the distributions differ. > Only difference between the above two steps is the information in the > settings file. > > What I understand to obtain the correct distributions we should use all the > non-bonded information in the settings file. Please correct me if I am > wrong. There is a typo in your settings.xml, type2=C instead of D. Anyhow after changing that I did: $ csg_stat --nt 8 --top topol.tpr --trj conf.gro --options settings.xml --cg pc_new_cg.xml $ csg_stat --nt 8 --top topol.tpr --trj conf.gro --options settings_all.xml --cg pc_new_cg.xml --ext dist_all.new and $ echo -e "a B?\na D?\nq" | make_ndx -f conf.gro $ echo -e "B?\nD?" | g_rdf -s topol.tpr -f conf.gro -n index.ndx -bin 0.01 If you now look at plot gnuplot> p "rdf.xvg" w l,"B-D.dist.new" w l, "B-D.dist_all.new" w l
you will see that rdf.xvg, B-D.dist.new and B-D.dist_all.new exactly the same. I am not sure where your original difference came from. The only things, which might make a difference is the "--begin 20", but you can do the same with the -"b- option of g_rdf. > >> >> We need to document that better, patch for the manual are welcome! >> <https://code.google.com/p/votca/wiki/Manual> >> > Are you suggesting me to incorporate patches to the manual. If so, I > followed the above link but could not figure out how can I do it. The "Contributing a change" paragraph tells you how to submit updates to the manual. As you have already built the manual in past, it should be an easy thing. Cheers, Christoph > > Chandan > > -- > 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.
