[gmx-users] g_MSD results for different sampling intervals

[Justin Lemkul]

On 2/25/15 4:00 PM, Carlos SOTO GARZA wrote:
> Dear Gromacs Users,
>
>
> I am trying to analyse the diffusion of a ligand in a polar solvent.
> Initially, I had 10 ns of sampling, which were later extended to 50 ns.
> I analysed the MSD (3D) when I finished the initial 10 ns and later, when I
> got the 50ns. To my surprise, the MSD plot for the initial 10ns does not
> overlap the plot for the MSD of the 50ns.

How different are the outcomes?  You're looking at the statistics of a single 
molecule, so convergence could be difficult.

-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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