[gmx-users] g_wham error

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 11 17:31:00 CEST 2009

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 = 

> 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.


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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


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