Mark, thanks for explanation. So if I understood that graph correctly I must define R1=1 and R2=2 values from my example 1<Rij<2 to obtain quadratic restrain forces done in my distance range ( from 1 to 2 angstr). In other words this would restrains the i and j atom to the desired distance by the force wich would increased by the quadratic progresion upon distance will increased up to 2. Does it correct ?
So the value R0 ( no forces= no restraints) must correspond to the values above and below my range. How the same range value for R0 could be defined ? JAmes 14 марта 2012 г. 3:42 пользователь Mark Abraham <mark.abra...@anu.edu.au>написал: > > > I can't think of a clearer way to explain the functional form of the > distance restraint than the given equation with an example graph of it > nearby. You have some distance range that you want to see happen based on > some external information. You need to choose the distance constants for > that functional form to reproduce that in a way that you judge will work, > given your initial distance. The linear regime above r_2 is useful for not > having forces that are massively large (from a quadratic potential) far > from the region of zero potential. Whether this is important depends on > your starting configuration. > > > >> >> I already answered this. >>> http://lists.gromacs.org/**pipermail/gmx-users/2012-**March/069301.html<http://lists.gromacs.org/pipermail/gmx-users/2012-March/069301.html> >>> >> I've found only theoretical explanation of such possibility ( >> gradually increasing force constant during simulation). But I >> intresting in practical implementation. Could I do it in scope of >> single MDrun by some options in mdm fle or should I do step-by-step >> series of simulation with gradually changing forces appplied on the >> disres in each MDrun? >> > > Only step by step. Something like simulated annealing is only available > for temperature variation. > > Mark > >> >> >> James >> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
-- 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