On Tue, Oct 27, 2015 at 1:02 PM, Fabian gmail <fabian.glaser.gmail.com>
wrote:
> So Jason,
>
> Would you recommend to run production with NVT?
>
Depends. I often do, but I don't always.
> The reason I used NPT was the protocol on the tutorial of MMPBSA on amber
> site uses it….
>
But the protocol doesn't use restraints... In any case, that's an example
that's not intended to serve as recommended real-world settings. You
always need SOME NpT simulations to make sure that the density stabilizes,
but after that the NVT/NpT distinction is often unimportant (remember that
excepting phase changes, the various ensembles are equivalent).
>
> If NVT is good enough, I will switch, since I understand it will also be
> quicker.
>
Marginally if you are using the Monte Carlo barostat (a little more
pronounced if you are using Berendsen on the GPU).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Oct 27 2015 - 10:30:08 PDT
