Hi Takahiro, this topic comes up again every now and then and has been discussed on the mailing list extensively on the mailing list. A good summary can be found here: <https://groups.google.com/d/msg/votca/3P8iT9UVBHg/gSTigVSQAwAJ>
In short, bonds, angles etc. in the mapping file generate exclusion automatically, in the same way as gromacs does. You can use $ csg_dump --top topol.tpr --cg map.xml --execl to figure out what VOTCA is doing. Cheers, Christoph 2016-04-25 5:09 GMT-07:00 Takahiro Ohkuma <[email protected]>: > Dear developers and users > > I am trying to make CG potentials for a homo-polymer system with IBI. > I found that the radial distribution function of CG beads calculated with > csg_stat shows different results when the bonded (angles / dihedrals) > interactions are defined or not in the mapping xml file. I guess some > neighbor beads are automatically excluded in calculating the RDF, and this > rule should hold in the IBI process. Is it right? How can I control the > exclusions? > > Thank you very much. > Takahiro Ohkuma > > -- > 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.
