[gmx-users] Is diffusion coefficient dependent on box size?

[Justin Lemkul]

On 10/12/15 10:49 AM, Pallavi Banerjee wrote:
> Hello Users,
>
> On simulating SPC-E water, I see that I get two different values of
> diffusion coefficient from two different box sizes. I get D=2.4 from a
> cubic box of 3 nm and D=2.7 from a cubic box of 7 nm. All the .mdp
> parameters are the same for both. The diffusion coefficients are obtained
> from g_msd Any idea what could be going wrong here?
>

There are finite size effects in computing diffusion coefficients.  See 
dx.doi.org/10.1021/jp0477147

-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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