CHARMM-GUI Enhanced Sampler for molecular dynamics simulations with collective variables and various enhanced sampling methods

Abstract

Molecular dynamics (MD) simulation is a robust tool to investigate complex biomolecular systems with all-atomistic representation. MD trajectory based on accurate force field and equations of motion integration gives us the molecular-level understanding of the target systems. However, one might not observe rare-events or slow-processes within the typical simulation time if high free barrier or kinetic trap presents. Various enhanced sampling methods have been developed and utilized to resolve this issue by modifying temperatures, adding non-equilibrium forces to the subset of the system, or reshaping underlying potential energy functions.