Recently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the probability density P(≈r) = < δ(r − ≈r) &>; associated with rate values≈r of a spatial coordinate r. In this Letter we extend their approach to the case of a general reaction coordinate ξ(r), an arbitrary function of the configuration-space coordinates. The generalized version is shown to be the integral form of the free energy calculation in the constrained-reaction-coordinate ensemble where the mean force is computed as an average in a ξ-constrained ensemble. The two approaches are shown to be of equal computational efficiency for a very simple Lennard-Jones test case.
Activation energies by molecular dynamics with constraints / Emanuele, Paci; Giovanni, Ciccotti; Ferrario, Mauro; Raymond, Kapral. - In: CHEMICAL PHYSICS LETTERS. - ISSN 0009-2614. - STAMPA. - 176:(1991), pp. 581-587. [10.1016/0009-2614(91)90259-C]
Activation energies by molecular dynamics with constraints
FERRARIO, Mauro;
1991
Abstract
Recently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the probability density P(≈r) = < δ(r − ≈r) &>; associated with rate values≈r of a spatial coordinate r. In this Letter we extend their approach to the case of a general reaction coordinate ξ(r), an arbitrary function of the configuration-space coordinates. The generalized version is shown to be the integral form of the free energy calculation in the constrained-reaction-coordinate ensemble where the mean force is computed as an average in a ξ-constrained ensemble. The two approaches are shown to be of equal computational efficiency for a very simple Lennard-Jones test case.
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