[gmx-users] PMF plot against distance

Justin Lemkul jalemkul at vt.edu
Thu Feb 20 12:20:41 CET 2014

On 2/20/14, 5:00 AM, Arunima Shilpi wrote:
> Dear Sir
> I have been working in umbrella sampling to analyse protein-ligand
> interaction and
> calculate Potential Mean Force (PMF).
> I have generated the following his.xvg file and have provided in the
> attachment. I request you to kindly guide me as to how to plot against
> distance.

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The PMF you get from g_wham is plotted as a function of whatever reaction 
coordinate you define.  If it is a vector, then you have PMF as a function of 
distance.  The default x-axis label from g_wham (last I checked) was, 
unfortunately, the letter "z," which is confusing.  It should actually be a 
Greek "zeta" to correspond with the typical reaction coordinate notation.  Zeta 
is whatever you define.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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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