Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations.

ABSTRACT: Traditional free energy calculation methods are well-known for their drawbacks in scalability and speed in converging results particularly for calculations with large perturbations. In the present work, we report on the development of biasing potential replica exchange multisite λ-dynamics (BP-REX MSλD), which is a free energy method that is capable of performing simultaneous alchemical free energy transformations, including perturbations between flexible moieties. BP-REX MSλD and the original MSλD are applied to a series of symmetrical 2,5-benzoquinone derivatives covering a diverse chemical space and range of conformational flexibility. Improved λ-space sampling is observed for the BP-REX MSλD simulations, yielding a 2-5-fold increase in the number of transitions between substituents com

SUBMITTER: Armacost KA 

PROVIDER: S-EPMC4731093 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature