[gmx-users] umbrella sampling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sat Jul 30 05:59:51 CEST 2011

format your data for 2D-WHAM with 1D being the distance and the 2nd-D  
being your other coordinate of interest. Specify a value of zero for  
the force constants for your 2nd-D. Run 2D-WHAM. Boltzmann project the  
2D PMF onto your 2nd-D.

I think you can also do essentially the same thing by re-weighting  
using the F-values from 1D-WHAM, but I find the above method to be the  
simplest. It also provides you with a 2D free energy profile, which  
can be informative both biologically and to indicate on sampling  

Note that you're very likely going to run into convergence problems  
since your 2nd-D will rely on brute-force to converge, and worse: the  
umbrellas in 1D can force the sampling in the 2nd-D to surmount energy  
barriers that might be circumvented in unrestrained sampling.


-- original message --

Qian Wang wrote:

I used umbrella sampling method to restrain the distance of two
molecules at several distances. Then I can use g_wham to get the free
energy as a function of the distance. Is there any way that I can get
the free energy as a function of another parameter? Thanks a lot.

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