If a simulation ensemble doesn't converge reliably over a given time scale, then it's not converged over that time scale. Repeating it from different starting conditions still adds valuable statistics, but can't be a replicate. Independent replicated observations of the same phenomenon allow you to assess how likely it is that your set of observations reflect the underlying phenomenon. The problem in sampling-dependent MD is usually in making an observation (equating a converged simulation with an observation).
Mark On Wed, Nov 21, 2012 at 8:12 AM, Albert <mailmd2...@gmail.com> wrote: > hello: > > I am quite confused on how to repeat our MD in Gromacs. If we started > from the same equilibrated .gro file with "gen_vel = no" in md.mdp, > we may get "exactly" the same results which cannot be treated as reasonable > repeated running. However, if we use "gen_vel=yes" for each round of > running, sometimes our simulation may not converged at our simulated time > scale and we may get two results with large differences. > > So I am just wondering how to perform repeated MD in Gromacs in a > correct way so that our results can be acceptably repeated? > > thank you very much. > Albert > -- > 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
