2013/6/18 <[email protected]>: > Dear Votca Users, > > I have started using the software some time ago and i successfully managed > to extract bonded parameters from atomistic into the coarse-grained - this > is done. > i have my peptide made of 90 residues - each residue is one bead, however I > wish to have nonbonded parameters for 5 types of beads (A, B, C, D, E). In > this case I will group my amino acids into given types of beads. > > As I can see the input for IBI method is a RDF e.g. A-A, A-B, B-B, etc (25 > in total). From atomistic I will get 90*90/2 = 4050 RDF between residues. In > order to get an input for IBI shall I take an average of of RDF for A-A, > A-B, etc (25 in total) from atomistic (4050 in total)? It will not reproduce > atomistic in this case of its average. Please, explain and advice me. I guess you need to average your 4050 rdf to get 25 averaged rdfs.
You could do that with csg_stat or g_rdf if your simulation was done with gromacs. Christoph PS: Sorry for the delay, this email slipped under my radar. > 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. > > -- 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.
