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

Justin Lemkul jalemkul at vt.edu
Mon Dec 15 03:43:09 CET 2014

On 12/14/14 9:33 PM, Victor Rosas Garcia wrote:
> Hello everybody,
> I'm back.  From the last time I tried this, I took all the
> configurations (all 500) and did the npt_umbrella equilibration.
> *Then* I was able to pick evenly spaced configurations (25 of them)
> and ran the md_umbrella. This is my histogram (g_wham does not
> complain about poor sampling anywhere):
> https://drive.google.com/file/d/0B2K7fedV_ZFzRF9qd2FsMTdrSm8/view?usp=sharing
> and my profile is still wrong
> https://drive.google.com/file/d/0B2K7fedV_ZFzUTZ6ZW54QXR5a2s/view?usp=sharing
> Perhaps I need to go up to 31 windows, like in the paper?

Yes, as is stated in the tutorial.  You won't get the same exact profile unless 
you do the same exact procedure.  The profile in the tutorial is merely an 
illustrative example; the tutorial itself is a quick and dirty version of the 
better sampling in the paper, done for didactic reasons.



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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