[gmx-users] g_wham error in umbrella simulation

Ming Tang m21.tang at qut.edu.au
Fri Apr 24 03:01:29 CEST 2015

Hi, Justin

You are right. Finally, I got both of the curves. Happy! 
Thanks for your guidance.

-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Justin Lemkul
Sent: Wednesday, 22 April 2015 10:18 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] g_wham error in umbrella simulation

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 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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