On the determination of rate constants from equilibrium molecular dynamics simulations

Abstract

In this article we consider the calculation of rate constants from equilibrium molecular dynamics simulations using the conformational isomerization in liquid butane as an example. In particular we discuss the method by which transition state theory estmates of the rate constant may be calculated from simulation data. Care has to be taken when calculating the average velocity along the reaction coordinate at the barrier. If this is computed just from actual barrier crossings we show that there is a systematic overestimation by a factor of exactly π/2. Further analysis has allowed the connection between the barrier crossing rate and the transition state theory value for the rate constant to be established. We compare rate constants determined by the ‘‘reactive flux’’ method with values obtained using alternative approaches applied to liquid n-butane [D. Brown and J. H. R. Clarke, J. Chem. Phys. 92, 3062 (1990)]. The results of this comparison have implications regarding the identification of the plateau value when using the reactive flux method. A straightforward procedure is described which can establish confidence limits for rate constants calculated in this way.