[gmx-users] umbrella sampling

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun May 30 14:14:54 CEST 2010

Dear Qian:

Debiasing equations for this can be found by analogy to eq. 16 and 17  
in the the original Torrie and Valleau US paper: "Nonphysical sampling  
distributions in Monte Carlo free-energy estimation: Umbrella sampling".

Alternatively, I used a simple method in  
doi:10.1016/j.cplett.2008.05.099 which was to run 2-dimensional WHAM  
with my quantity of interest as the second dimension, but assigning  
this second dimension a force constant of zero.

Be careful with either method, though, as apparent convergence of the  
free energy does not imply convergence of all other observables.


-- original message --


I am using Gromacs 4.0.5 for umbrella sampling. I know that I can use  
g_wham to calculate the free energy along the constrained distance. Is  
there a command in Gromacs 4.0.5 that can calculates the average of  
any other obserble (for example, potential energy) along the  
constrained distance? Thanks a lot.


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