Constraints make the job of the minimizer more difficult. If the starting configuration is bad enough that the EM step might be really useful, give the potential energy surface a free run without constraints. And then in such cases do a preliminary NVT with dt=0.0005 and no constraints to get things relaxed further. Only once things are close to correct do you want to think about constraints so you can increase the time step.
Mark On Fri, Jun 14, 2013 at 12:38 PM, maggin <maggin.c...@gmail.com> wrote: > Hi, Justin, > > Thank you very much for your help! > > Another question is when we do steep minimization, if it will be better > first do steep with constraint, then do steep without constraint? > > Thank you very much! > > maggin > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Steepest-Descents-in-vacuo-tp5009143p5009152.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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 > -- 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
