[gmx-users] Unbiased or biased

Justin Lemkul jalemkul at vt.edu
Mon Mar 27 19:00:01 CEST 2017

On 3/27/17 11:02 AM, m g wrote:
> Dear Justin Lemkul,I red your tutorial "Umbrella Sampling", I want to know
> about unbiased and biased method. you sad that used biasing potential. which
> parameter in md files refers to biased? how can i used unbiased method? what

An applied external potential is a bias, i.e. the harmonic restraint being 
applied by the pull code.

> is difference between unbiased and biased exactly? I used this method that
> you learned in this tutorial for pulling a drug molecule across the POPC
> membrane, but I don't know in my work this PMF is unbiased or biased. would
> you pleas help me?Thanks

The simulations that generate the distance distributions are biased because 
there is an external potential applied to them.  The PMF, by definition, is 
unbiased (this the point of WHAM, and if you haven't read the Kumar paper and 
those cited within, stop what you're doing and read those now).



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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