Studying the affinity and kinetics of molecular association with molecular-dynamics simulation
- 8 January 2003
- journal article
- research article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 118 (4), 1821-1827
- https://doi.org/10.1063/1.1530162
Abstract
Given a long molecular dynamics trajectory which consists of hundreds of association and dissociation events, the theoretical formulas to calculate the affinity and dissociation rate constant are presented. The derivation is based on the survival function of the associated complex, and it emphasizes the nearest-neighbor distribution function. The applicability of this brute-force approach is demonstrated by the simulation of methane association in water.Keywords
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