[gmx-users] How to calculate protein-surface interaction energy

[Justin Lemkul]

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
> Gromacs.

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

-- 
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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
http://mackerell.umaryland.edu/~jalemkul

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