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
This publication has 13 references indexed in Scilit:
- Bimolecular kinetics according to a stochastic analysis of reactant dynamicsThe Journal of Chemical Physics, 2001
- The statistical-thermodynamic basis for computation of binding affinities: a critical reviewBiophysical Journal, 1997
- Computational Methods to Predict Binding Free Energy in Ligand-Receptor ComplexesJournal of Medicinal Chemistry, 1995
- A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic MoleculesJournal of the American Chemical Society, 1995
- Neighborship partition of the radial distribution function for simple liquidsThe Journal of Chemical Physics, 1992
- Nearest-neighbor distribution functions in many-body systemsPhysical Review A, 1990
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983
- Ion pairs and complexes: Free energies, enthalpies, and entropiesJournal of Chemical Education, 1969
- Diffusion of Methane, Ethane, Propane, and n-Butane in Water from 25 to 43°The Journal of Physical Chemistry, 1965
- ber den gegenseitigen durchschnittlichen Abstand von Punkten, die mit bekannter mittlerer Dichte im Raume angeordnet sindMathematische Annalen, 1909