[gmx-users] PMF calculation using g_wham using different simulation boxes

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 2 13:08:18 CET 2009

Li Jianguo wrote:
> Hi
> I am trying to calcualte the potential of mean force between two 
> polyatomic particles using umbrella potential and the g_wham command. I 
> need to run multiple windows from close to far inter-particle distance. 
> To save time, I used smaller box sizes for those windows with shorter 
> inter-particle distance, and larger box sizes for those windows 
> with longer inter-particle distance. Then I have multiple pullf files 
> and tpr files with different box sizes.
> I am wondering if using different simulation systems is acceptable when 
> applying g_wham command for PMF calculation.

I have never heard of such a thing.  Is the restraint distance always less than 
1/2 the box dimension in the pulling direction?  If not, then this approach 
doesn't work.

I have always been under the impression that when running umbrella sampling, you 
have to actually be doing sampling in different regions of configurational space 
in the same system, in order to get a continuous energy function and appropriate 



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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