[gmx-users] Analysis program g_wham

Justin Lemkul jalemkul at vt.edu
Wed Nov 19 19:14:56 CET 2014

On 11/19/14 12:02 PM, Kevin C Chan wrote:
> Dear Users,
> I am trying to use umbrella sampling results from NAMD to compute PMF versus distance using g_wham. However as I would not have the corresponding tpr files, I plan to stick to the -ip option. However I am not sure about the exact format of pdo file. Does anyone have experience on this?

The help information from g_wham explains the format, but it's rather tedious to 
put together and some people have reported issues with .pdo reading (though the 
threads tend to die, so we have no idea if there's actually a problem). 
Probably it's easier to use Alan Grossfield's WHAM for non-Gromacs data files. 
No special format required.



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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