[gmx-users] Simulation at Different pH's

Justin Lemkul jalemkul at vt.edu
Fri May 29 19:15:02 CEST 2015

On 5/29/15 9:05 AM, xy21hb wrote:
> Dear all,
> I would like simulate a protein-water binary system at different pH's.
> The protein is quite typical, could be lysozyme. So no need to worry about proton transfer.

Proton transfer can occur for any titratable group; I wouldn't necessarily 
assume it to be irrelevant.

> Should I still try constant-pH or any simpler methods available?

"Constant pH" specifically refers to techniques in which protonation states can 
change.  If you're looking solely at pH in terms of dominant protonation states, 
then just setting up the topology to reflect the dominant forms of all 
titratable groups is easy enough, and is commonly done.



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


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