Exploring, refining, and validating the paradynamics QM/MM sampling.

ABSTRACT: The performance of the paradynamics (PD) reference potential approach in QM/MM calculations is examined. It is also clarified that, in contrast to some possible misunderstandings, this approach provides a rigorous strategy for QM/MM free energy calculations. In particular, the PD approach provides a gradual and controlled way of improving the evaluation of the free energy perturbation associated with moving from the EVB reference potential to the target QM/MM surface. This is achieved by moving from the linear response approximation to the full free energy perturbation approach in evaluating the free energy changes. We also present a systematic way of improving the reference potential by using Gaussian-based correction potentials along a reaction coordinate. In parallel, we review other re

SUBMITTER: Plotnikov NV 

PROVIDER: S-EPMC12401620 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature