[AMBER] Replica Exchange pH simulations with explicit solvent

From: Jon Uranga <jonur9.gmail.com>
Date: Fri, 20 Sep 2019 12:07:55 +0200

Dear Amber users,

I am interested in running Replica Exchange pH simulations with explicit
solvent to evaluate pKa values at different systems. I am running it in
GPUs, but I am somewhat doubtful when setting the system up: should I use
NPT, NVT with periodic boundaries or a non periodic system?

I have observed that currently it is not possible to set ntp > 0 for REMD.
Indeed, when taking a look at the tutorial by Jason Swails (
http://jswails.wikidot.com/ph-remd) I have noted that they run it without
periodic boundary conditions. However, when considering explicit solvent
molecules (http://jswails.wikidot.com/explicit-solvent-constant-ph-md) in
the tutorial I think they employ igb=0, ntp=0 and ntb=1 for the production
phase (since they are not present in the input and therefore, the default
values will be used), which corresponds to NVT ensemble.

My concern is that without NPT ensemble one could not really get the Gibbs
Free enery, which I think it is very important for the evaluation of the
pKa and that it is eventually evaluated in every Monte Carlo step for this
particular type of simulation, if I am not mistaken.

Thereby, I would like to ask which would be the most suitable way of
running Replica Exchange pH simulations with explicit solvent. One could
use NVT ensemble, still using the periodic boundary conditions, but in this
case the Helmholtz Free energy would be obtained, and I am not sure how
meaningful this could be. Alternatively, one could use non periodic system.

Many thanks for your help!

Best regards,

Jon Uranga

Jon Uranga
Institute of Physical Chemistry
Computational Chemistry and Biochemistry Group
Tammannstr. 6
37077 Göttingen
Office Phone: 33131
E-mail: jon.uranga.chemie.uni-goettingen.de
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Received on Fri Sep 20 2019 - 03:30:02 PDT
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