[gmx-users] Wrong profile obtained in umbrella sampling tutorial
Victor Rosas Garcia
rosas.victor at gmail.com
Tue Nov 18 23:31:31 CET 2014
Thanks, I'll check it out. It may be a remnant of a previous, botched, run.
2014-11-18 15:56 GMT-06:00 Justin Lemkul <jalemkul at vt.edu>:
> On 11/18/14 3:23 PM, Victor Rosas Garcia wrote:
>> Sorry about that Office messup.
>> These are the new links:
>> 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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