W dniu niedziela, 30 czerwca 2013 23:59:18 UTC+1 użytkownik Victor Rühle napisał: > > 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 > > Thank you. The thing is that i want to exclude neighbors from atomistic in my RDF based on which I will build my CG potential. I have 6 groups in my system. Those residues are in a different places obviosuly. If I will exclude neighbors in g_rdf (which will happen by not putting one of them in the index file) I will exclude also long range interaction with other bead being much far away. Does votca have an advanced tool with such exclusions?
Steven > 2013/6/20 <[email protected] <javascript:>> > >> 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] <javascript:>. >> To post to this group, send email to [email protected] <javascript:> >> . >> 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.
