Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.

ABSTRACT: Molecular dynamics with coarse-grained models is nowadays extensively used to simulate biomolecular systems at large time and size scales, compared to those accessible to all-atom molecular dynamics. In this review article, we describe the physical basis of coarse-grained molecular dynamics, the coarse-grained force fields, the equations of motion and the respective numerical integration algorithms, and selected practical applications of coarse-grained molecular dynamics. We demonstrate that the motion of coarse-grained sites is governed by the potential of mean force and the friction and stochastic forces, resulting from integrating out the secondary degrees of freedom. Consequently, Langevin dynamics is a natural means of describing the motion of a system at the coarse-grained level and

SUBMITTER: Liwo A 

PROVIDER: S-EPMC8465211 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature