2013/7/1 <[email protected]>: > > > W dniu poniedziałek, 1 lipca 2013 15:04:38 UTC+1 użytkownik Christoph > Junghans napisał: >> >> 2013/7/1 <[email protected]>: >> > >> > >> > W dniu poniedziałek, 1 lipca 2013 02:51:23 UTC+1 użytkownik Christoph >> > Junghans napisał: >> >> >> >> 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. >> > >> > >> > 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? If you are using the same grid for input and output, the y points won't change. Linear interpolation will just draw lines between the given points. If you have distributions made of multiple Gaussian, why don't you fit multiple Gaussians to it and write the result out as a table again.
> > Does Votca 1.2.3 supports IBI for bonded or shall I upgarde it to 1.3 ? Bonded IBI only works in Votca 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 [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. >> > >> > >> >> >> >> -- >> 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. > > -- 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.
