2016-02-11 8:41 GMT-07:00 Christoph Junghans <[email protected]>: > 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. Also have a look at: <https://groups.google.com/d/msg/votca/3P8iT9UVBHg/NMnfVbnNAgAJ>
> > 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 -- 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.
