[gmx-users] g_wham .tpr / .xvg / .dat conversion issues

[Justin A. Lemkul]

On 1/6/10 1:51 PM, V Hariharan wrote:
> Hello All,
>
> I am trying to use g_wham to view the PMF for my simulation.  I read the
> g_wham -h help menu, and it requires .dat input files for the -if and
> -it input options.  My output files from mdrun for -s and -pf were .tpr
> and .xvg files, respectively.  How to I convert my .tpr and .xvg files
> into .dat files for use with g_wham?  Thanks!
>

 From g_wham -h:

"* With option -it, the user provides a file which contains the
   filenames of the umbrella simulation run-input files (tpr files),
   AND, with option -ix, a file which contains filenames of
   the pullx mdrun output files. The tpr and pullx files must
   be in corresponding order, i.e. the first tpr created the
   first pullx, etc."

The .dat files are thus ones that you must create; they are not automatically 
generated by mdrun or any other utility.

-Justin

> -- Venk
> __________________________________
> Venkatesh Hariharan
> Columbia University | Biomedical Engineering
> Graduate Research Assistant
>
> "You must be the change you wish to see in the world."
> --Mohandas Karamchand Gandhi
>

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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