Journal of Chemical Physics, Vol.109, No.18, 7737-7744, 1998
Free energy from constrained molecular dynamics
Activated processes can be studied in the molecular dynamics (MD) approach by imposing a mechanical constraint on the corresponding reaction coordinate and by performing a kind of thermodynamic integration. The blue-moon ensemble method provides us with the correct algorithm for computing the potential of mean force and the transmission coefficient. Here we show a procedure for;obtaining the mean force directly from the average force of constraint and a geometric correction term which is easy to compute in MD simulations. Previous work on the same problem will be also discussed.