At least upgrade to the latest release in the series (5.1.4) or better
yet, the actual latest version (2016.4) to see if this is a bug that's
been fixed. I seem to recall this same behavior reported before and
subsequently solved, but haven't dug it up.
-Justin
On 11/13/17 7:11 AM, Jefferies D.F. wrote:
Hey guys,
Sorry if it seems that I'm bumping this thread, but I was wondering if anyone
had any other suggestions before I let this thread die.
Thanks.
________________________________________
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Jefferies D.F.
[dfj1...@soton.ac.uk]
Sent: Thursday, November 02, 2017 1:29 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham
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-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Justin Lemkul
[jalem...@vt.edu]
Sent: Thursday, November 02, 2017 11:10 AM
To: gmx-us...@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
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
==================================================
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