[gmx-users] acidic pH

[Justin Lemkul]

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

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Justin A. Lemkul, Ph.D.
Postdoctoral Associate

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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