[gmx-users] How to generate generic data files for g_wham

[Justin A. Lemkul]

Ragnarok sdf wrote:
> I have finished a simulation using the pull code, but found nothing in 
> the manual or discussion list (regarding Gromacs 4) on how to create the 
> generic data files used as input for g_wham. I have only the two .xvg 
> files from -pf and -px generated from mdrun.

 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."

For example, tpr-files.dat:

pull0.tpr
pull1.tpr
pull2.tpr
...

pullf-files.dat:
pullf0.xvg
pullf1.xvg
pullf2.xvg
...

If you have just a single pullf.xvg and pullx.xvg, then you've sampled one 
window, and the output from g_wham will be nonsense.

> Another question is about what would be the difference between the -df 
> and the -dx files?

What are -dx and -df?  Do you mean -pf and -px?  Plot them and see :)

-Justin

> Thank you in advance
> Fabrício Bracht
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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