On Wed, Oct 2, 2013 at 3:22 AM, Christoph Junghans <[email protected]>wrote:
> 2013/10/1 Chandan Choudhury <[email protected]>: > > > > > > On Tue, Oct 1, 2013 at 8:34 PM, Christoph Junghans <[email protected]> > > wrote: > >> > >> There is a typo in your settings.xml, type2=C instead of D. > >> Anyhow after changing that I did: > > > > Thanks. It worked for me now. > >> > >> $ 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. > > > > The distribution matches very well. > Also if I change min to 0.45, the distribution still match exactly. > So I cannot really reproduce what happens for you before. > Thanks for troubleshooting. Few things were unknowingly mistaken. 1. I did not use the information of dihedrals in the exclusions. The exclusion list was different. This might have added to the different distribution. 2. The typo you figured out. Thanks for this. I now crossed checked with changing the min, it did reproduce the distribution. Thanks a lot once again. Chandan > > >> > >> > >> > > >> >> > >> >> 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. > > > > I will give a try. > >> > >> > >> Cheers, > >> > >> Christoph > >> > >> > >> > >> > >> -- > >> 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. > > > > > > 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. > -- 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.
