Hi, On Tue, Aug 25, 2015 at 5:08 AM PER HENRY ANDREAS WITTLER < 17526...@students.latrobe.edu.au> wrote:
> There is mentioned that for re-running an MD run for better statistics, it > can be good to change starting coordinates, besides the seed, is there a > gmx command which is used for randomly change starting coordinates of a pdb > file? > Not really. You can e.g. generate your solvent box in different ways, but MD is so chaotic that you really don't need to do this. Look at the time series of your observable from two runs with different velocities, and observe that their decorrelation time is much shorter than your equilibration time. I need such a command or script for a PBS script which automatically goes > through all gmx setup commands to start and run an arbitrary number of > following MD production runs, assumed that all steps are working. I've > also made it to replicate and change seeds automatically for velocity > generation for three seeds, starting automatically. So three tests started > with one bash script, and one clean-up script resetting everything. It is generally more efficient to do your preparation (via a script) on some local resource (or the PBS login node), and transfer only the .tpr file(s) to run with mdrun on the PBS resource via the PBS submission script. Mark -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
