[gmx-users] Question for bdc = xy

[Justin Lemkul]

On 3/27/14, 7:31 PM, ookami a wrote:
> I want my system to be simulated in only two dimension periodic boundary
> condition. but for this one, after the pvt, everything spread in the whole
> box(where z_direction is 3 times the original length of the box) and the
> vacuum disappeared. so i think this system is still simulated with xyz
> dimension.
>

The only thing your results indicate is that the molecules in it diffused to 
fill the available volume.

-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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