[gmx-users] Define box size

[Justin Lemkul]

On 1/1/15 2:21 AM, Seera Suryanarayana wrote:
> Dear gromacs user
> I have one protein with 254 residues. I would like to simulate this protein
> in solvent system. For that first we need to define box by editconf. My
> question is how does we define box size?
>

The box size should be set to avoid minimum image convention violations, so in a 
sense the box-solute distance is related to the longest cutoff.

http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention

-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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