Fwd: [gmx-users] umbrella Sampling and PMF- Error estimation

Justin Lemkul jalemkul at vt.edu
Wed Jul 31 17:15:17 CEST 2013

On 7/31/13 10:19 AM, Mohsen Ramezanpour wrote:
> Dear Dr.Justin
> I read that article, It was very helpful. Thanks a lot.
> After using g_wham with bootstrapping options.
> I have got an averaged PMF profile (like Fig.2C in that article) and
> an standard deviation (like Fig.2D In that article) which obtained in
> this way.
> As you see, the standard deviation is equal to zero at Z=1.5 nm
> (because I defined all PMFs as Zero at that point) and it is around 2
> kj/mol in Z=0.25
> Since I am interested to Gibbs Binding Free Energy(GBFE) (the
> difference between the Gibbs energy of these points, Z=.0.25 &1.5 nm),
> Is it right to say the error for estimating of GBFE is 2 kj/mol ?

I would suggest you do a bit of reading about propagation of error, and you will 
have your answer.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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