Free-energy calculations - Theoretical Biophysics Group

Reaction coordinate–based free-energy calculations Measuring the error associated to an ABF calculation
Midpoint rule: ∆A −∆ξ
p
〈Fξ〉ξi
i=1
Average and variance of the force over the reaction pathway:
⎧
⎪⎨
⎪⎩
µ = 〈Fξ〉ξ = 1
σ
p 1
〈Fξ〉ξi =
p
p
i=1
p
µi
i=1
2 = 1
p
σ
p
i=1
2 2
i + (µ − µi)
Fluctuation on the free-energy difference:
〈|∆A − ∆A| 2 〉 = (∆ξ) 2
p ni
nj 1
〈(F
ninj
i,j=1 k=1 l=1
i ξ,l − µ)(Fi ξ,k − µ)〉
(∆ξ) 2
p p
σ
N
i=1
2 i + (µ − µi)
2 2 p2
+ 2σ
N κ
Standard deviation: 57 σ∆A ∆ξ σ
(1 + 2κ)1/2
N1/2 57 RODRIGUEZ-GOMEZ ET AL. (2004)
Chris Chipot Free-energy calculations