Re: [AMBER] NPT equilibration at constant pH with protonation states allowed to change

From: Jason Swails <>
Date: Fri, 11 Nov 2016 12:39:05 -0500

On Fri, Nov 11, 2016 at 12:31 PM, Eric Lang <> 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.


Jason M. Swails
AMBER mailing list
Received on Fri Nov 11 2016 - 10:00:03 PST
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