Path sampling with memory reduction and replica exchange to reach long permeation timescales.

ABSTRACT: Assessing kinetics in biological processes with molecular dynamics simulations remains a computational and conceptual challenge, given the large time and length scales involved. For kinetic transport of biochemical compounds or drug molecules, the permeability through the phospholipid membranes is a key kinetic property, but long timescales are hindering the accurate computation. Technological advances in high-performance computing therefore need to be accompanied by theoretical and methodological developments. In this contribution, the replica exchange transition interface sampling (RETIS) methodology is shown to give perspective toward observing longer permeation pathways. It is first reviewed how RETIS, a path-sampling methodology that gives in principle exact kinetics, can be used to c

SUBMITTER: Vervust W 

PROVIDER: S-EPMC10398259 | biostudies-literature | 2023 Jul

REPOSITORIES: biostudies-literature