[gmx-users] Performing protein-ligand GROMACS MD under pH 5 conditions

Justin Lemkul jalemkul at vt.edu
Mon Mar 10 10:46:12 CET 2014

On 3/10/14, 5:29 AM, MUSYOKA THOMMAS wrote:
> Dear Users,
> I am doing MD simulations involving lysosomal proteins catalases and small
> organic compounds and would be glad to know how I can achieve this under a
> pH=5 environment.

The concept of pH isn't well defined in standard MD.  The best you can do is 
protonate the constituent residues according to their pKa values to get the 
predominant forms of the proteins at that pH.  Approaches like constant-pH MD 
might be useful; see the numerous threads in the archive on this topic.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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