[gmx-users] g_wham error in umbrella simulation

Ming Tang m21.tang at qut.edu.au
Wed Apr 22 13:38:35 CEST 2015

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

-----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: Monday, 20 April 2015 10:17 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] g_wham error in umbrella simulation

On 4/19/15 9:53 PM, Ming Tang wrote:
> Dear all,
> I am doing an umbrella simulation, and come across the following error.
> Command line:
>    g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 
> 2000
> Found 27 tpr and 27 pull force files in tpr-files.dat and 
> pullf-files.dat, respectively Reading 13 tpr and pullf files Automatic 
> determination of boundaries...
> -------------------------------------------------------
> Program g_wham, VERSION 5.0.4
> Source code file: 
> /home/tm/Downloads/gromacs/src/gromacs/gmxana/gmx_wham.cpp, line: 1767
> Fatal error:
> . Should be tpr, xvg, or pdo.0.tpr

Is this a copy/paste problem or is this really what the line said?  The error message should be "Unknown file of type (something). Should be tpr, xvg, or pdo."  Note the "0.tpr" that is tacked on to the end and the lack of preceding text.  Any weird line endings in your tpr-files.dat file?  Check and run dos2unix if needed.  The presence of "0.tpr" somewhat suggests the very first line is causing a problem, even though it appears gmx wham understands how many files it should find; it just can't determine the right file names/types.


> For more information and tips for troubleshooting, please check the 
> GROMACS website at http://www.gromacs.org/Documentation/Errors
> tpr-files.dat:
> umbrella0.tpr
> umbrella137.tpr
> umbrella155.tpr
> umbrella163.tpr
> umbrella169.tpr
> umbrella174.tpr
> umbrella179.tpr
> umbrella185.tpr
> umbrella199.tpr
> umbrella206.tpr
> umbrella223.tpr
> umbrella239.tpr
> umbrella257.tpr
> umbrella275.tpr
> umbrella291.tpr
> umbrella308.tpr
> umbrella324.tpr
> umbrella344.tpr
> umbrella369.tpr
> umbrella383.tpr
> umbrella392.tpr
> umbrella422.tpr
> umbrella450.tpr
> umbrella463.tpr
> umbrella479.tpr
> umbrella497.tpr
> umbrella499.tpr
> pullf-files.dat
> pullf0.xvg
> pullf137.xvg
> pullf155.xvg
> pullf163.xvg
> pullf169.xvg
> pullf174.xvg
> pullf179.xvg
> pullf185.xvg
> pullf199.xvg
> pullf206.xvg
> pullf223.xvg
> pullf239.xvg
> pullf257.xvg
> pullf275.xvg
> pullf291.xvg
> pullf308.xvg
> pullf324.xvg
> pullf344.xvg
> pullf369.xvg
> pullf383.xvg
> pullf392.xvg
> pullf422.xvg
> pullf450.xvg
> pullf463.xvg
> pullf479.xvg
> pullf497.xvg
> pullf499.xvg
> I used this method several times before, and did not come across this problem. could anybody tell me where is the problem?
> Thanks


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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