On Fri, Nov 11, 2016 at 12:31 PM, Eric Lang <eric.lang.bristol.ac.uk> wrote:
> Hello,
>
> I want to run some explicit solvent pH-REMD simulations, and I just want to
> check if, after the heating phase, I can run a NPT equilibration at a
> constant pH with the protonation states allowed to change.
>
NpT + REMD in Amber is not supported for any kind of REMD. Furthermore,
every replica *should* have exactly the same box size when doing REMD with
PBC. This is because the exchange criteria does not incorporate
volume/pressure contributions, as I believe would be required to correctly
sample from the desired distribution.
The proper procedure to use is to run a *single* replica until you get a
stabilized and sensible density, then build each replica from that starting
point using NVT the rest of the time.
HTH,
Jason
--
Jason M. Swails
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Received on Fri Nov 11 2016 - 10:00:03 PST
