[gmx-users] peculiar water behavior

[Justin Lemkul]

On 6/17/14, 5:20 PM, Chetan Mahajan wrote:
> Thanks, Justin. That makes it clear. I have one small question: I do not
> know how does position restraint algorithm work with other things in
> gromacs, but  doesn't it generate a lot of stress due to slab moving from
> center to near box boundary despite of position restraints, when -com
> option is used for refcoord-scaling? If there is a lot of stress, would
> this stress affect simulation results?
>

You can get a sense of that by extracting the energy associated with the 
restraints from the .edr file.

-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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