Dear All, Please any suggestion?
regards, On Mon, Jun 3, 2013 at 4:53 PM, gromacs query <gromacsqu...@gmail.com>wrote: > Dear All, > > (Sorry for long mail!) > > (Thanks Thomas Schlesier for clarifying previous umbrella queries) > > I wish to run umbrella samplings using restart file of previous window. > e.g. initial distance between A (reference) and B (pulled group) is 1 nm > (10 Angs) then I intend to run 10 windows after each 1 Angstrom. Due to > some reasons I want to use restart file of previous window, so if suppose > 1st window (10 Angstrom window) is done then I will use last restart file > of 1st window for 2nd window (9 Angstrom window) > > (This is different from Justin's tutorial in which initial configurations > are generated in single pulling experiment). > > In such case as I said I want to use last restart of 1st Window for 2nd > window so obviously the distance will not be exactly 9 Angstrom between A > and B for 1st window restart file. What approach I should use for adjusting > initial distance being 9 Angstrom to get initial configuration for 2nd > window > > Knowing the distance between A and B in the restart file of 1st window > (say 'x') > then for second window y = 9 - x (where x can be > or < 9), > > > First approach: > > pull_rate1 = (y/1000) or even slower > > > Second approach: > > pull_init1 = y > pull_rate1 = 0.0 > > > Please Note for both the cases I can use pull_vec1 or pull rates (- or +) > for positive or negative relative movement to get exact 9 Angstrom window > distance > > regards, > Jiomm > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
