Re: AMBER: constant-pH MD with replica exchange

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Thu, 11 Oct 2007 11:33:30 -0400

Maciek,

We have been working on this, and will be sending a paper out next week
for publication.

Basically, Amber 9 cannot do this as distributed, but we hope to have
the code in for the next release.

Doing constant pH and replica exchange in pH space turns out to be
inefficient in terms of sampling conformational space.

So, what we do is to run constant pH MD doing REMD at different
temperatures. Since the protonation state of a residue can be different
in different temperatures, one needs to be very careful with the
exchange equations, but it all works out ok.

Adrian


Maciej Dlugosz wrote:
> Dear Amber developers/users:
>
> Is this possible to run constant-pH MD with
> replica exchange?
> Has anyone tried?
>
> Thanks,
>
> maciek
>
>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Sun Oct 14 2007 - 06:07:25 PDT