Efficient Empirical Valence Bond Simulations with GROMACS.

ABSTRACT: We describe a protocol to perform empirical valence bond (EVB) simulations using GROMACS software. EVB is a fast and reliable method that allows one to determine the reaction free-energy profiles in complex systems, such as enzymes, by employing classical force fields to represent a chemical reaction. Therefore, running EVB simulations is basically as fast as any classical molecular dynamics simulation, and the method uses standard free-energy calculations to map the free-energy change along a given reaction path. To exemplify and validate our EVB implementation, we replicated two cases of our earlier enzyme simulations. One of these addresses the decomposition of the activation free energy into its enthalpic and entropic components, and the other is focused on calculating the overall cata

SUBMITTER: Oanca G 

PROVIDER: S-EPMC10500987 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature