[gmx-users] Computing of reaction coordinate by g_wham

Justin Lemkul jalemkul at vt.edu
Wed Nov 18 13:42:14 CET 2015

On 11/18/15 4:08 AM, Damiano Buratto wrote:
>   Dear Gromacs users,
> please, is there someone that can help me to understand how g_wham compute the reaction coordinate of pulled group?
> I would like to compute the PMF for the passage of a molecule through a channel (with spatial restraint) using the umbrella sampling (US) technique. I built the windows for the US by looking at the centre of mass (COM) of the pulled molecule in a way that any window is at 1A of distance from the former. When the US was finished, I run g_wham (with reference group on the channel) and I saw that the histograms of the windows are not centred where I supposed they should be (the centre are not at 1A of distance one from the other, and the value is different from the COM of the pulled group less the COM of the reference group). Moreover, if I run g_wham in the verbose mode I can see that the position associated with each US window is a bit different from the value I expected (but in agreement with the centre of the histograms).

The reaction coordinate and window positions are read from the .tpr files you 
provide to g_wham.  If these aren't what you expected, you likely set something 
up wrong.  grompp provides lots of useful information when you're building the 
.tpr files, so start by checking to make sure that information matches your 



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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