2013/7/1 <s.neuman...@gmail.com>: > > > W dniu poniedziałek, 1 lipca 2013 15:28:35 UTC+1 użytkownik Christoph > Junghans napisał: >> >> 2013/7/1 <s.neu...@gmail.com>: >> > >> > >> > W dniu poniedziałek, 1 lipca 2013 15:04:38 UTC+1 użytkownik Christoph >> > Junghans napisał: >> >> >> >> 2013/7/1 <s.neu...@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 >> > >> > >> > 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. > > > Thank you. I tried to fit in another software my potential to 6th order > polynomial but results are not promising... which option of csg_stat will > fit it to multiple gaussian? There is no VOTCA tools doing that, but you could use scipy or gnuplot.
>> >> >> > >> > 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! See: <https://code.google.com/p/votca/wiki/Installing#Development_Version> > > > I will upgrade it. For bonded do we provide both distributions and > potentials in settings? > > <cg> > <bonded> > <name>angle</name> > <min>1</min> > <max>3</max> > <step>0.05</step> > <inverse> > <target>angle.dist1.tgt</target> > <gromacs> > <table>table_a1.xvg</table> > </gromacs> > </inverse> > </bonded> > > So the input are both refined table_a1.xvg as well as angle.dist1.tgt? Will > they be updated every step? angle.dist1.tgt is the target distribution against which csg_inverse compares the current distribution, it is never updated. table_a1.xvg is the table to export VOTCAs internal potential to, it is updated every iteration step. > > Thanks, > > Steven > >> > >> > >> >> >> >> > >> >> > 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. >> >> > 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. >> > 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.
