[gmx-users] g_wham error in umbrella simulation

[Justin Lemkul]

On 4/22/15 4:46 AM, Ming Tang wrote:
> Hi, Justin
>
> Thanks a lot. Dos2unix works. There is even no blank space in every line. The
> problem is that I downloaded those .dat files from the internet, which were
> created in windows system. But I got another problem. Following your umbrella
> sampling tutorial, I got the PMF curve. The trend of the curve is quite close
> to that of the curve in the tutorial. But, the ΔG is -31, 20 more compared to
> -50.5 in the tutorial. Besides, I only get one histogram, the data of the

You won't get the value in the tutorial unless you follow the published 
protocol.  The tutorial is an abbreviated version of a more complex protocol 
involving (1) prior simulation of 100 ns and (2) asymmetrical window 
distribution.  I believe this should be stated already in the tutorial.

> rest histograms are zero (one horizontal line). Do you have any suggestions
> for me about what's wrong with my simulation?

You're probably just not plotting the histogram file right.

xmgrace -nxy histo.xvg

to show all the histograms.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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