[gmx-users] PMF calculation by umbrella sampling simulations
mpi566 at gmail.com
Thu Apr 30 06:43:22 CEST 2015
With GMX 4.6.5, I tried to reproduce a system of the dissociation of
a single peptide in an AB42 protofibril with PMF (potential of mean
force) calculation in Justin's umbrella sampling tutorial. He
derived the binding energy from PMF from a series of umbrella sampling
simulations and obtained a value of free energy close to -50.5
kcal mol-1. But I got a value of -37.5 kcal mol-1 after PMF
curve was converged. The value difference is significant and this
raises two questions. What dose cause this difference of ~13 kcal mol
-1 ? although I used GPU for calculations, which is the only
modification (cutoff-scheme = Verlet). What is a reasonable range of
binding free energy in this case of AB42 protofibril ?
The umbrella histogram showing the overlap between window looks
reasonable. See attached here.
Suggestions or opinions are appreciated.
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