[gmx-users] Problem using gmx wham

[Justin Lemkul]

On 11/1/17 4:26 PM, Jefferies D.F. wrote:
> Hi,
>
> I am attempting to use gmx wham to compute a potential of mean force. I have used the command line:
>
> gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kJ
>
> where tpr-files.dat and pullf-files.dat contain a list of the .tpr and pullf.xvg files from each umbrella sampling window, respectively.
>
> It seems that gmx wham is having trouble reading the .tpr and .xvg files, as I get this error message:
>
> -------------------------------------------------------
>
> Program gmx wham, VERSION 5.1.4
>
> Source code file: /local/software/gromacs/5.1.4/source/gromacs-5.1.4/src/gromacs/gmxana/gmx_wham.cpp, line: 1800
>
>
> Fatal error:
>
> Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.
>

The extra space after "tpr" in the printed error suggests something is 
weird with the input .dat file. Did you create it with a proper plain 
text editor? What about running dos2unix on it to make sure you've got 
the right kind of line endings?

-Justin

> For more information and tips for troubleshooting, please check the GROMACS
>
> website at http://www.gromacs.org/Documentation/Errors
>
> -------------------------------------------------------
>
>
> I have computed potential of mean force profiles before (using this Mac), but I haven't encountered this problem. Could someone help me with this problem?
>
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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