[gmx-users] Problem using gmx wham
Jefferies D.F.
dfj1g14 at soton.ac.uk
Tue Nov 14 15:38:36 CET 2017
Hi Justin,
Thanks for your response. I've attempted to run gmx wham using GROMACS 5.1.4 and I seem to get the same problem, even if I attempt to use dos2unix before I issue a command i.e.
-------------------------------------------------------
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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
I've taken a look at older posts relating to this problem, and I saw that a similar complaint was resolved after the poster used dos2unix (following your recommendation). But that hasn't seemed to work for me.
Regards,
________________________________________
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: Tuesday, November 14, 2017 2:35 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Problem using gmx wham
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-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Jefferies D.F. [dfj1g14 at soton.ac.uk]
> Sent: Thursday, November 02, 2017 1:29 PM
> To: gmx-users at 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-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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==================================================
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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