On Thu, 2015-08-13 at 14:58 +0800, whb wrote:
> Hi all：
>
> I have a question about the method of pH-REMD. I’ve read the paper
> published in JCTC(J. Chem. Theory Comput., 2014, 10 (3), pp 1341–1352).
>
> It said that the probability of accepting these replica exchange attempts,
> given by eq 3, depends only on the difference in the number of titrating
> protons present in each replica and their respective difference in pH
>
>
>
> I think that it contains an assumption that the residue in lower pH can be
> more protonated. But I think that pka of the residue depends the environment
> where the residue exists in the protein. And when the proteins structure has
> changed severely in lower pH , the residue may have another pH in that
> situation. And this situation may contradict with the assumption the theory
> contains.
There are indeed a lot of assumptions made in any MD simulation --
pH-REMD included. However, the *replica* exchange acceptance
probability that you refer to is derived directly by solving the
detailed balance equation of the probability distribution functions for
the semi-grand canonical ensemble. Therefore, this is one of the few
aspects of the simulation that is, in fact, *not* an approximation and
is exact.
The effect of the protein environment is accounted for by the
protonation state change attempts *within* a replica (keep in mind there
are two Monte Carlo change attempts being made -- one between
protonation states and the other between replicas). I present an
abbreviated derivation of this equation on my Wiki:
http://jswails.wikidot.com/ph-remd#toc16 and there are also more
detailed explanations about replica exchange in general as well as the
basic theory underlying constant pH simulations in my dissertation:
http://jswails.wdfiles.com/local--files/about/jms_Dissertation.pdf
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 13 2015 - 06:00:03 PDT
