[gmx-users] Wrong profile obtained in umbrella sampling tutorial

Justin Lemkul jalemkul at vt.edu
Tue Nov 18 22:56:43 CET 2014

On 11/18/14 3:23 PM, Victor Rosas Garcia wrote:
> Sorry about that Office messup.
> These are the new links:
> histogram
> https://drive.google.com/file/d/0B2K7fedV_ZFzaFlOMWh1QXFTa2s/view?usp=sharing
> profile
> https://drive.google.com/file/d/0B2K7fedV_ZFzSm16bnlJSUFGVms/view?usp=sharing
> I understand that the profile may not look exactly the same between
> different runs, but I do think the difference is large enough to think
> something is amiss.

Sampling in window 1 is a little odd - the distribution is incredibly narrow, if 
you can even call it a distribution at all.  Make sure everything is OK in that 
window.  In the absence of a well-defined minimum, you're not going to get a 
sensible profile.  People's mileage varies as far as recapitulating that PMF 
curve, but I have received confirmation from at least two other people that the 
PMF can be reproduced following the method in the paper.



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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