[gmx-users] how to repeat simulation correctly?

[Mark Abraham]

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 <mailmd2011 at 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
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