[gmx-users] Problem using gmx wham

[Jefferies D.F.]

Hi Justin, 

Thanks for the response. The .dat files were created with the vi text editor, they contain lists of the .tpr and .xvg to be read, e.g.

umbrella0.tpr
umbrella1.tpr
umbrella2.tpr
..
umbrella52.tpr 

I've tried to use dos2unix,  i.e. 
~> dos2unix tpr-files.dat
and 
~> dos2unix pullf-files.dat

but I still get the same error message i.e. 

-------------------------------------------------------
Program gmx wham, VERSION 5.1.2
Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 1800

Fatal error:
Unknown file type of umbrella52.tpr . Should be tpr, xvg, or pdo.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

That being said, it seems you're correct in thinking something's weird with the input files. After I created new .dat files, I got this message:

-------------------------------------------------------
Program gmx wham, VERSION 5.1.2
Source code file: /Users/Damien/Downloads/gromacs-5.1.2/src/gromacs/gmxana/gmx_wham.cpp, line: 3610

Fatal error:
Found 53 file names in tpr-files.dat, but 54 in pullf-files.dat

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

gmx wham is registering 54 files, when only 53 were written.  





________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Justin Lemkul [jalemkul at vt.edu]
Sent: Thursday, November 02, 2017 11:10 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham

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.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================

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