W dniu poniedziałek, 1 lipca 2013 15:04:38 UTC+1 użytkownik Christoph Junghans napisał: > > 2013/7/1 <s.neu...@gmail.com <javascript:>>: > > > > > > 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 >
Thank you a lot! csg_resample --type linear will use linear function which is not desired... My distributions are made of multiple gaussian distributions so i guess akima (deafult) option? Does Votca 1.2.3 supports IBI for bonded or shall I upgarde it to 1.3 ? > > > > 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+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.
