Revisiting the Exact Relation between Potential of Mean Force and Free-Energy Profile
W. den Otter. Journal of Chemical Theory and Computation9 (9):
Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulations, but they subtly alter the phase space distribution. In a recent letter of a related title in this journal, Wong and York J. Chem. Theory Comput. 2012, 8, 3998â4003 suggest replacing Fixmanâs mass-metric correction with its inverse and adding a Jacobian contribution to the potential of mean constraint force. This letter refutes both suggestions, discusses the underlying interpretation problems, and provides supporting numerical simulations.