Many thanks David!
And do we actually need nscm=5000 using langevin dynamics like in my case?
Cheers,
Enrico
Il giorno ven 5 ago 2022 alle ore 14:23 David A Case
<david.case.rutgers.edu> ha scritto:
>
> On Fri, Aug 05, 2022, Enrico Martinez wrote:
>
> >Regarding your last comment, in fact I've just changed the duration of
> >the simulation by increasing the number of steps producing a
> >trajectory of 500 ns. Assuming that the aim is to calculate dG of the
> >ligand binding using MMGBSA approach, what values should be reasonable
> >for ntpr=5000, ntwr=5000, ntwx=5000, ntwe=5000, nscm=5000?
>
> First, be sure to check (e.g. visually) that your trajectory at 330K makes
> good sense. There is no point in evaluating energies if something goes
> wrong at this elevated temperature.
>
> Second, 50,000 snapshots is a lot for most mm-gbsa calculations. Consider
> setting ntwx to 25,000 (say). You don't need to set ntwr -- that pretty
> much just wastes time. And I don't think you need ntwe.
>
> Alternative: keep ntwx at 5000, but do an initial simulation for 100 ns,
> rather than 500. See what you learn from the energies and fluctuations
> for the shorter run. You can always do a longer run later.
>
> ....dac
>
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Received on Fri Aug 05 2022 - 06:30:04 PDT
