[gmx-users] acidic pH
jalemkul at vt.edu
Sun Jul 14 21:53:09 CEST 2013
On 7/14/13 2:23 PM, fatemeh ramezani wrote:
> Hello dear users
> I'm simulating gold nanoparticle interaction with protein. I want to change the pH of system. What would need to be changed to simulate this system at pH 3.0?
As is discussed frequently on this list (hint: check the archive for some very
good discussions), the concept of pH in an MD simulation system is relatively
ill-defined in a classical simulation. Protonation states are fixed in normal
MD, so the only thing you can really do is approximate the effect of pH by
protonating the amino acids in their most prevalent form at that pH.
Justin A. Lemkul, Ph.D.
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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