[gmx-users] How to calculate protein-surface interaction energy
jalemkul at vt.edu
Sat Oct 18 15:06:00 CEST 2014
On 10/18/14 8:51 AM, James Lord wrote:
> Hi Justin,
> Thanks for the prompt answer. I selected LJ-(SR) but I am getting a
> positive fluctuating line over the simulation time. Looking at the vmd
> movie I can see that protein (Lysozyme) is coming into contact with surface
> afte 10ns and is 5 nm away at the beginning?? my surface is a not charged
> (polyethylene)?? I'd expect zero energy at beginning and upon touching the
> surface negative value??? any comments? Sorry this has nothing to do with
A few things:
1. Make sure your index groups are correctly constructed.
2. What does 5 nm correspond to? A COM distance? A minimum distance? If the
latter, then the LJ-SR energy should likely be zero, but if it's a COM distance,
that's not necessarily the case.
3. Is your PE model united-atom or all-atom? If the latter, you still have
partial charges that will contribute to a negative Coul-SR (of course, this is
something you can check very simply)
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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