[gmx-users] pmetune and restarting

Mark Abraham mark.j.abraham at gmail.com
Fri Dec 12 18:14:20 CET 2014

On Fri, Dec 12, 2014 at 5:23 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
> Hi.
> I notice that after I stop a simulation by specifying the number of hours
> that it runs with -maxh,
> and then restarting the simulation, at the beginning of each restart, the
> pme is tuned again.
> Will that cause any error if I periodically restart the simulation? How big
> is the error?

If the tuning is designed to implement PME by varying the parameters in a
conservative and intended-as-iso-accurate way (which it is), then what
problem could arise from repeated tuning? See brief discussion in 3.17.5 of
manual. Assessing the impact of that tuning would require that you first
have assessed how

Is it possible to save and reuse pme tune result by a mdrun option?

You can observe the result and construct your input .mdp file to use that
fourier grid and cutoff values and then use mdrun -notunepme. But now you
are hard-coded for that machine running on that many nodes under that
external network load.


Thank you.
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