Re: [AMBER] Constant protonation vs. constant pH simulation

From: Adrian Roitberg <>
Date: Sat, 26 Jun 2010 14:24:17 +0200

Dear nicholus

It all of course depends on your guess at the constant protonation states.

For instance, if you are simulating a protein at pH=10, then keeping the
glu and asp residues as unprotonated if a very good bet. In that case,
doing a constant protonation MD (with unprotonated asp/glu) and running
a constant pH MD should give you the same sampling of conformational space.

But, if you are simulating at ph=4, then, since the pka of glu and asp
is somewhere around 4 most of the time, there is NO SINGLE constant
protonation state that can accurately reflect the correct physics of the

On 6/26/10 2:19 PM, nicholus bhattacharjee wrote:
> Dear community,
> As we know there are two ways of doing
> simulation of proteins in AMBER: constant protonation and constant pH. My
> query is that will the trajectories be of vast difference when we apply
> this two methods in the same protein? Or will the conformation at different
> time steps remain similar with marginal deviations? Thank you in advance.

                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry
                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email
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Received on Sat Jun 26 2010 - 05:30:04 PDT
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