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. 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
