2013/7/1 <[email protected]>: > > > 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? Use csg_stat, which can also calculate bonded distributions. You will need to add bonds (in the mapping file) between the beads, which you want to exclude.
Christoph > > Steven > > > >> >> 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. > > -- 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/groups/opt_out.
