[gmx-users] Creating box,

[Justin Lemkul]

On 2/3/15 8:32 PM, Bishnu Acharya wrote:
> Dear Gromacs User,
>
> I am new in Gromacs. I want to create rectangular box like dimensions 5.0
>   5.0  15.0 and want to put nonane-water-nonane on it. I mean there layers
> first nonane and water and again nonane layers.

There aren't two nonane layers, because the nonane is continuous via PBC.  So 
really you just have a simple biphasic system.  Conveniently, there's a tutorial 
that illustrates how to do that:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html

-Justin

-- 
==================================================

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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