Good Rates From Bad Coordinates: The Exponential Average Time-dependent Rate Approach.

ABSTRACT: Our ability to calculate rate constants of biochemical processes using molecular dynamics simulations is severely limited by the fact that the time scales for reactions, or changes in conformational state, scale exponentially with the relevant free-energy barrier heights. In this work, we improve upon a recently proposed rate estimator that allows us to predict transition times with molecular dynamics simulations biased to rapidly explore one or several collective variables (CVs). This approach relies on the idea that not all bias goes into promoting transitions, and along with the rate, it estimates a concomitant scale factor for the bias termed the "CV biasing efficiency" γ. First, we demonstrate mathematically that our new formulation allows us to derive the commonly used Infrequent Met

SUBMITTER: Mazzaferro N 

PROVIDER: S-EPMC11270837 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature