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
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