Let me explain it this way. I used csg_stat with my AA topol.tpr and trajectory and supplied xml files to get rdf between my beads but what I get was a sharp peak. This peak happened in distance equal toaverage bead length of my molecules beads. I guess it is becuase tpr file of AAMD does not contian bonds. As I created tpr file based on my CG top, and started to get my RDF I got it right. I think for the case of hexane something like this should happend but as beads with similar name are located in a larger distance it is not obvious. Anyway I did not check this for hexane! so I am not sure.
On Wednesday, February 10, 2016 at 7:50:26 PM UTC-6, Christoph Junghans wrote: > > 2016-02-10 16:48 GMT-08:00 Alireza Moradzadeh <[email protected] > <javascript:>>: > > I mean getting rdf from an AAMD trajectory. > > > > > > On Wednesday, February 10, 2016 at 6:48:04 PM UTC-6, Alireza Moradzadeh > > wrote: > >> > >> Dear All, > >> > >> I think votca has a bug using csg_stat to get rdf of between beads > within > >> one moleculs Let me explain it in this way. > >> > >> I used votca to get rdf for my molecule which has three beads A B C > >> I find out that there is a jump in rdf in the range of bond between > these > >> beads > >> > >> RDF(A,B) > >> > >> Did anybody have a similar problem? > You have to provide some more information! E.g. some plots. > Can you reproduce the bug by using the atomistic input from the hexane > example? (see hexane/atomistic folder). > Have you checked that the exclusion using csg_dump? > Remember that without a mapping file csg_stat doesn't generate any > exclusion, but is just reads the one from the tpr file. > Opposite if you use a mapping file, bonds and angles in settings xml > will automatically generate exclusions, but nothing else will be > excluded - you can check that using csg_dump with a mapping file. > > Christoph > > > >> > > -- > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
