[gmx-users] Choosing more PMF-windows

[Justin A. Lemkul]

Shay Teaching wrote:
> Distance of zero between COM of pull_group0 and pull_group1?
> 

Yes.  The x-axis of the histogram plot indicates the distance along the reaction 
coordinate.

-Justin

> On Sun, Jul 31, 2011 at 5:46 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Shay Teaching wrote:
> 
>         Dear GROMACS users,
> 
>         I have recently completed running several PMF-windows.
>         After viewing the histrogram file it seems that I need better
>         sampling at some positions, but the histogram file starts at z=0.
>         Is there any way to prevent g_wham from starting at 0, and
>         instead show the real Z-coordinates of the selected-group?
> 
> 
>     If it starts at zero, then it means your sampling starts at a
>     distance of zero along the reaction coordinate.  If this is not what
>     you intended, check your input files.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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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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