[gmx-users] g_wham error

[Justin A. Lemkul]

Ragnarok sdf wrote:
> 
>     Ragnarok sdf wrote:
>      > While trying to analyse my several windows with g_wham the
>     following error
>      > appears :
>      >
>      > Fatal error:
>      > Pull geometry direction not supported
>      >
>      > my entry files consist on the several px.xvg listed in a .dat
>     entry file and
>      > the several .tpr from each of the simulations also listed in a
>     tpr.dat file
>      >
> 
>     Right, but error is coming from the .tpr files, themselves, sort of.
>     Unfortunately g_wham only works when you've specified "pull_geometry
>     = distance"
>     in the .mdp file.  Maybe this should be documented somewhere?
>      g_wham -h does
>     not make this clear.
> 
>     -Justin
> 
> I could not find it in g_wham -h. So now i only need to change from 

Hence my frustration, some time ago :)

> "pull_geometry  = direction" to "pull_geometry = distance"? Is the 
> outcome going to be the same?

No idea.  But by using g_wham, you can only get results with "pull_geometry = 
distance."

> Do I need to include the first simulation in the g_wham analysis? By 
> first simulation I mean the one I used to separate the dimers and not 
> the ones I have simulated at each starting distance obatined from 
> withing the previous one.
> 

No.  That would not make sense, since the forces are continually changing over 
time.  The WHAM method for umbrella sampling calculates PMF from restraining 
configurations in pre-defined sampling windows, not those in which positions are 
continually changing.

-Justin

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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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