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

From: Eric Lang <eric.lang.bristol.ac.uk>
Date: Fri, 11 Nov 2016 17:31:56 +0000


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.

I don't think it should matter for the pH-REMD to start the replicas with a
common equilibrated structure that is not fully protonated but perhaps this
would lead to a poor protonation state sampling during REMD? (After this
NPT equilibration I would use the resulting structure to start a quick
CpHMD NVT equilibration at each pH I want to run my replicas and then start
the pH-REMD per se).

Does anyone have tested such kind of approach or know, based on experience,
that this would be a bad idea?

I can give more details about why I want to do such kind of equilibration
if needed.

Many thanks in advance for your help,


Eric Lang
BrisSynBio Postdoctoral Research Associate Modelling
Centre for Computational Chemistry
School of Chemistry - University of Bristol
Bristol BS8 1TS - United Kingdom
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Received on Fri Nov 11 2016 - 10:00:02 PST
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