[gmx-users] g_WHAM

Shima Arasteh shima_arasteh2001 at yahoo.com
Tue Aug 20 15:59:19 CEST 2013


I have a tpr-files.dat containing 5 tpr files as it:

Also the pullf-files.dat is in accordance with tpr-files.dat.
But when I run g_wham and visualize the histo output, I see only one curve and not 4 curves which are expected to have appropriate overlaps! Would you please let me know how come? Is it usual to get one curve from each histo.xvg?

Thanks for your suggestions. I appreciate you in advance.


From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Thursday, August 8, 2013 11:08 PM
Subject: Re: [gmx-users] g_WHAM

On 8/8/13 2:37 PM, Shima Arasteh wrote:
> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCalvv
> It's the error what get;
> File input/output error:
> tpr-files.dat

Then a file named "tpr-files.dat" does not exist in the working directory. 
Check for typos and the existence of the file.


> Sincerely,
> Shima
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Thursday, August 8, 2013 10:45 PM
> Subject: Re: [gmx-users] g_WHAM
> On 8/8/13 2:13 PM, Shima Arasteh wrote:
>> Hi,
>> Would you please let me know if it is possible to get just the first 2 histograms of total 24 histograms by running g_WHAM?
>> I mean the tpr-files.dat contains only 2 .tpr files of umbrella sampling simulations and not the all.
>> I ran such dat file, but doesn't work and gives me an error of no input file.
> The exact error, copied and pasted from the terminal, is more useful.
>> g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal
> As long as pullf-files.dat and tpr-files.dat both specify the same number of
> input files and the .tpr and .xvg files therein match, there should be no problem.
> -Justin


Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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