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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Dec 2 14:42:36 CET 2009

Hi Li,

In my opiniun, what you propose is acceptable, but not rigorous, and  
you will need to prove that there are no unexpected artifacts of  
changing box size. For example, you should definitely run a couple of  
your small box systems as larger boxes as well and show that you get  
the same histograms for the distances between your polyatomic particles.

Justin is correct about the need for a box that is 2x larger than your  
displacement, and pull_pbcatom is an important option to set as well.


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  


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