2013/7/1 <s.neuman...@gmail.com>: > > > W dniu poniedziałek, 1 lipca 2013 02:51:23 UTC+1 użytkownik Christoph > Junghans napisał: >> >> 2013/6/18 <s.neu...@gmail.com>: >> > 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? For g_rdf, you could use a special index file or create a tpr with additional exclusion.
In csg_stat you could add bonds (in the mapping xml file) between the beads, which you want to exclude. > 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? csg_resample uses akima spline by default, but it can also do cubic spline or linear interpolation. > 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? use csg_resample with --type linear and --derivative file option. Christoph > > 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. >> > To post to this group, send email to vo...@googlegroups.com. >> > 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. > > -- 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.
