[gmx-users] Regarding umbrella samplling

Justin Lemkul jalemkul at vt.edu
Tue Nov 25 13:31:24 CET 2014

On 11/25/14 1:23 AM, Sathish Kumar wrote:
> Hai gromacs users,
>                               Can we use the direction-periodic mdp option
> while running the samplling of windows instead of distance. The distance
> option was giving error that
> Distance of pull group 1 (15.017257 nm) is larger than 0.49 times the box
> size (15.033495) .
> So, for all windows can i use the option direction-periodic instead of
> distance.

You can use whatever geometry makes sense.  There is no reason to believe that 
any particular geometry is inherently "right" or "wrong" for any given purpose, 
and generally speaking, if utilized properly, you can usually use any of the 
geometry options to achieve equivalent effects.



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


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