[gmx-users] My box size canges somehow

[Justin Lemkul]

On 4/8/14, 9:50 AM, Vytautas wrote:
> Open nvt.xtc you will see water molecules filing larger than initial space.
> In my opinion that is wrong or at least I do not want that.
>

Your initial box (from em.gro) is incompletely filled; there is void space in 
all directions.  The water moves around to fill that.  Fill the box properly 
with water or resize the box to fit the contents of the system.

-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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