W dniu poniedziałek, 1 lipca 2013 02:51:23 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/6/18 <s.neu...@gmail.com <javascript:>>: > > 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. >
Thank you. I think I need to calculate rdf between different types specified in Gromacs... however, residues are neighboring so I wish to exclude those interactions. In gromacs g_rdf does not have this option (-cut option will just cut the distance which is incorrect). Would g_stat be able to exclude neighbors from my atomistic? Another issue: I used BI for angles - I tried refining my potential using VOTCA but it somehow describes it poorly... Does csg_resample use a function to refine it? What kind of function? I would prefer to refine it my own but no clue how I will then calculate the derivative of those values (3rd column in table)a*.xvg). Would you advise? Steven > > > 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+un...@googlegroups.com <javascript:>. > > To post to this group, send email to vo...@googlegroups.com<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 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.
