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

[Justin Lemkul]

On 10/20/14 8:11 AM, James Lord wrote:
> Hi Justin,
> Would you please tell me from the files I sent you which of them you
> checked and how you got to the conclusion that  (I mean which command )
> "This system behaves correctly - there is a zero interaction energy (both
> Coulomb and LJ) at t=0, so it is fine".

mdrun -s bLac_rerun_interactionenergy.tpr -nsteps 0

The Protein-C10 energy terms are all zero at the initial step, e.g. step 0.

-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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