Dear Steven, I don't think there is a general rule when you should exclude beads. I have seen cases where the 1-5 non-bonded interactions were treated separately via an artificial "bond" to mimic the different behaviour of non-bonded interaction within the chain.
>From the technical point of view: If you add bonded interactions to the mapping file, VOTCA will automatically exclude these groups when evaluating the rdf. If you don't do mapping, it will use the exclusion list from the gromacs topology, so you could provide a modified topology with customized exclusion lists. You can always check which beads are excluded via csg_dump --excl Best, Victor 2013/6/20 <[email protected]> > Hello, > > I successfully extracted bonded parametrs for my protein CG model based on > the atomistic simulation. In my CG I have 6 different beads, each > corresponding to one amino acid. I want to calculate cumulative RDF (radial > distribution functions) between them as an input to IBI. > I group them in 6 beads running RDF... however I feel I should exclude > groups which are really close as it will influence RDF too much and the > potential - 1-3 interactions should be omitted, On the other hand groups I > want to exclude will interact with given group which is more far away. is > there any rule for exclusions in these case? I will appreciate your help. > > Steven > > -- > 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/groups/opt_out. > > > -- 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/groups/opt_out.
