[gmx-users] window spacing in umbrella sampling
jalemkul at vt.edu
Fri Jan 6 20:42:46 CET 2017
On 1/6/17 2:22 PM, faride badalkhani wrote:
> Dear GROMACS users,
> I have performed pulling simulations on polymer-drug complex an each window
> was obtained by an increment of 1 Å from the previous window, and for each
> window, 5 ns MD simulation was performed. But the histogram for the first 6
> windows is as follows:
> I am very beginner in Umbrella sampling. Could you tell me how should I
> change the sampling to get a reasonable histogram, please?
The windows are not evenly spaced and/or the force constant is insufficient to
maintain the desired restraint distances. You have mostly redundant windows
with a huge gap. You may need more windows, better/different spacing, and/or
different force constants.
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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