[gmx-users] Genbox question

[Justin Lemkul]

On 11/3/14 11:39 PM, Kevin C Chan wrote:
> Dear Users,
>
> I am trying to build some starting structures of lipid bilayers for MD using
> genbox to add waters. For some reasons I have already equilibrated my lipids
> in a water box previously so it no longer looks like a perfect rectangle,
> there are “flying tails" at the edges. However I still want to build a
> typical bilayer-in-water model in which water only appears above and below
> the bilayer (but not asides) and it should be able to introduce a periodic
> boundary condition in the x-y plane  (assuming the bilayer’s normal is along
> the z-axis) afterwards. The problem is as I could not accurately define the
> dimensions of my equilibrated lipids anymore, how could genbox be used to
> fill the box as what I expected?
>

Take the box vectors from the corresponding frame of the previous simulation 
that you've used.

-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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