[gmx-users] umbrella sampling

[chris.neale at utoronto.ca]

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.

Chris.

-- original message --

Hi,

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.

Sincerely,
Qian