Membrane Permeability of Sucrose Calculated from Equilibrium Time-Correlation Functions Using Molecular Dynamics Simulations with Enhanced Sampling.

ABSTRACT: A computational framework for rigorously computing the membrane permeability of small molecules from unbiased molecular dynamics simulations is presented. The method in its optimized form exploits the committor probability within the transition path theory framework and is applicable to molecules with free energy barriers for which a determination of the permeability coefficient from spontaneous crossings during equilibrium simulations would be unfeasible. A novel computational protocol is implemented through which the equilibrium time-correlation function is calculated from a combination of enhanced sampling to determine the equilibrium potential of mean force of the permeant molecule and a reweighted ensemble of short unbiased trajectories. By extracting the steady-state flux from commit

SUBMITTER: Harris J 

PROVIDER: S-EPMC12721406 | biostudies-literature | 2025 Jul

REPOSITORIES: biostudies-literature