[gmx-users] A small Questions of umbrella samping

Justin Lemkul jalemkul at vt.edu
Sat Dec 6 05:10:03 CET 2014

On 12/5/14 10:54 PM, vg wrote:
> Dear gromacs users
> I read the tutorial of umbrella sampling and have a small question I don't know
> I do a umbrella samping simulation as the tutorial show us, the pmf image also like the tutorial result .
> But I was read another papers like the explain paper of g-wham: JCTC 2010.6 3713-3720. The pmf image have a immediately move up in figure 1&2 。
> How could I get the pmf image like this? do I need to take more window in the high energy barrier position or just use some commands behind the g-wham or modify the map file ?
> Look forward reply and thank you very much

I presume you mean that the energy minima are well defined with a steep increase 
at small values along the reaction coordinate.  The tutorial example does not 
have such a well defined minimum because you can't physically force the protein 
chains any closer; it is impossible to stably sample very small values of the 
reaction coordinate, though an energy minimum becomes defined with sufficient 
sampling.  The PMFs you refer to are for very simple, small molecules, which can 
sample short COM distances.

> P.S. i take the two figure in attachment please check.

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> Your sincerely  Cao
> China ,TianJin, Nanking university
> School of physics
> Ph.d
> 发自我的 iPad


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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