[gmx-users] Lennard-Jones potential not matching with published data

[Justin Lemkul]

On 7/23/14, 2:40 PM, ibrahim khalil wrote:
> Dear gromacs users, i know this is not a good question to post here but i
> am trying to reproduce some published data where the Lennard-Jones
> potential is plotted with respect to time.
>
> In my simulation, my results are about half (not exactly half but around
> half) of the published data. I am stuck here for like a month and cannot
> find my mistakes.
>
> Can anyone help me where to look for my mistake? I am using a modified
> oplsaa forcefield.
>
> Should i check my forcefield parameters? Or my mdp parameters?
>

I would suspect the force field.  Do some simple test to confirm - two LJ 
particles in a box at different distances so you can plot the energy.  If that 
confirms what you expect, increase complexity according to whatever you're doing.

-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 601
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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