[gmx-users] Potential Energy is positive on minimizing the system

[Justin Lemkul]

On 2/23/17 8:29 AM, Anurag Dobhal wrote:
> Thank you. Should I not use PME and PBC while performing simulations in
> Vaccum ?
>

No, you should not.  Use no PBC and infinite cutoffs (all cutoffs set to zero) 
to mimic vacuum conditions.  Otherwise you're simulating some type of diffusely 
occupied crystal environment.

-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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