Don't know, but re-interpreting the old velocities at a new time might not be fully integrated with things calculated from the old velocities, such as temperature-coupling quantities. For switching integrators, you will need to re-equilibrate, so you may as well generate new velocities and avoid the problem.
If you want to suggest fixing any possible problem, please file an issue at redmine.gromacs.org Cheers, Mark On Thu, Jun 6, 2013 at 4:38 AM, Sikandar Mashayak <symasha...@gmail.com>wrote: > Hi > > I first performed a simulation using leap-frog integrator, which went well > and got the expected results. For post-processing I want velocities at full > time step, but, as per my understanding, leap-frog computes and writes > velocities at half-time step. Therefore, I just changed integrator from > 'md' to 'md-vv', i.e., velocity verlet. Unfortunately, after this change in > .mdp file (i.e. keeping all other settings exactly same as previous > leap-frog run) when I run 'mdrun' I am getting 'nan' in output from the > first step itself. > > So I am wondering what could be the reason for this behavior of 'md-vv' > integrator. > > Thanks > Sikandar > -- > 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
