A method of incorporating rate constants as kinetic constraints in molecular dynamics simulations.

ABSTRACT: From the point of view of statistical mechanics, a full characterization of a molecular system requires an accurate determination of its possible states, their populations, and the respective interconversion rates. Toward this goal, well-established methods increase the accuracy of molecular dynamics simulations by incorporating experimental information about states using structural restraints and about populations using thermodynamics restraints. However, it is still unclear how to include experimental knowledge about interconversion rates. Here, we introduce a method of imposing known rate constants as constraints in molecular dynamics simulations, which is based on a combination of the maximum-entropy and maximum-caliber principles. Starting from an existing ensemble of trajectories, ob

SUBMITTER: Brotzakis ZF 

PROVIDER: S-EPMC7812743 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature