W dniu poniedziałek, 1 lipca 2013 15:07:02 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/7/1 <[email protected] <javascript:>>: > > > > > > 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 >
Thanks a lot! For example, I have 4 beads neighboring of type A (A1, A2, A3, A4) disrupted by one type B (B1) - this is repetative. Hence, If calculating RDF of A-A I wish to exclude A1-A2 and A1-A3, A2-A4, A4 - A3 interactions - in general 1-2 and 1-3 interactions. Shall I make artificial bonds in mapping file then between 1-3 beads? Steven > >> > > > > 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] <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. > > > > > > > > -- > 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.
