2015-10-11 11:42 GMT-06:00 frank Zack <[email protected]>: > Hi, > > i created a coarse grained representation of a large polymer (appended) by > biased mc. I dont have an atomistic representation of that system. So i > created a "pseudo"-topo file and a "pseudo"-mapping file. > I applied the hexane/ibi_bonded example to my system, but I guess I made > some mistake in the mapping file (why do i need this it all for csg_stat?) > because csg_stat doesnt find any angles. You need a mapping for two reasons, VOTCA isn't able to read bond/angle names from the topology files because these things are usually not named. And VOTCA bond and angle definition are a bit more general as it could be averages over multiple bonds/angles and virtual bonds between e.g. end to end beads, which are not in the topology.
> > Pls see the attached files. Is there any obvious mistake? The trajectory > file is too large (46 MB) for uploading here. You can get it here: > https://www.dropbox.com/s/lmzir99zkth5srt/traj.xtc?dl=0 > > this is how i use csg_stat: > > ~/votca/bin/csg_stat --options ./settings.xml --top step_001/topol.tpr --trj > step_001/traj.xtc --cg hexane_cg.xml --begin 10 > > no errors occur. but angle-dist is empty. It is hard to say what went wrong, but my guess is that the beads triples listed in the angle block inside cg_bonded block somewhere towards the end of the file are wrong. You can use $ csg_dump --top topol.tpr --cg hexane_cg.xml to see what bead types VOTCA sees. > > thx for any advice, > > regards,frank > > -- > 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/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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
