2013/9/30 Chandan Choudhury <[email protected]>: > Dear votca users, > > I am iterating the non-bonded part of the polymer (with following sequence: > A1-B1-C1-B2-D1-B3-C2-B4-D2-B5-C3-E1). In step_001, my observations are > following: > > csg_stat uses the following command to compute the distributions : > > csg_stat --nt 8 --options > /data/home/chandan/Documents/votca/polycarbonate/trimer/mapping_II/re/ibi/nb/B_D/settings.xml > --top topol.tpr --trj traj.xtc --begin 20 --first-frame 0 > > I obtain the distributions in B-D.dist.new file. Here in settings.xml, the > min is 0.37 > > When, I change the min to 0. It gives the exact distribution. > > But, when I try to include the information of all the other bonded and > non-bonded interaction (min=0.0 and max values), then I need to use a > mapping file (attached). > csg_stat --nt 8 --options settings_csg_stat.xml --top ../topol.tpr --trj > ../traj.xtc --begin 20 --first-frame 0 --cg ../../pc_new_cg.xml > > Here, the setting contains all bonded and non-bonded part with min=0.0. The > distribtution I obtain is B-D.dist_withpc-xml.new. > > I also tried the g_rdf tool (with nrexcl=3). The output file is B-D.rdf.xvg. > Here the selection are between all B's and D's. > > It can be seen that the distribution obtained are different. On using > coarse-grained xml and when I donot use it, the distributions are different. > The gmx tool also gives the different result. > > Am I doing something wrong. I can suspect the problem might be in the cg > mapping file. But, I am unable to locate it. Can some one help me. > > The trajectory and tpr is same for all the above commands. The trajectory is missing, just send a conf.gro. One frame will be enough to check for the error.
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 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 We need to document that better, patch for the manual are welcome! <https://code.google.com/p/votca/wiki/Manual> Cheers, Christoph > > Chandan > -- > 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.
