2016-02-10 19:17 GMT-08:00 Alireza Moradzadeh <[email protected]>: > 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. Are you using a mapping file? Or are acting purely (without mapping) on the atomistic coordinates? In the former case, you will need to add bonds and angle to the mapping file (see https://groups.google.com/d/msg/votca/NDvv-iPsL0I/LAoapPJOcBQJ for a more detailed discussion). In the latter case, you need to check the exclusion with csg_dump and maybe modify your top file.
Christoph > 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]>: >> > 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]. >> > 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. >> >> >> >> -- >> 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. -- 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.
