[gmx-users] pH during free energy calculation

[Justin Lemkul]

On 2/9/15 7:42 AM, vivek sharma wrote:
> Dear Experts and users,
> I am running simulation for solvation free energy calculation using
> thermodynamic integration approach (as mentioned in Justin's tutorial). My
> system consist of a cation molecule, an anion molecule and bulk of solvent
> molecules.
> I want to understand the pH of my system, what will be the default pH for
> such a system? It will be helpful if anybody can comment on such a
> simulation and help in understanding pH behavior of such systems?
>
> Waiting for useful comments and insights from the community.
>

There are no exchangeable protons in a classical MD simulation, so there is no 
pH.  There are constant pH simulations, but those are fundamentally different. 
See the numerous discussions on this topic in the archive.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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