Coarse-grained Biomolecular Simulations

Abstract

Towards cellular-scale structural modeling, multiscale biomolecular simulation is gaining much attention. Here, I review methodological aspects of coarse-grained (CG) biomolecular simulations. I begin with conceptual argument of coarse graining for proteins where the idea behind Gō models is discussed. Then, statistical physics and theories of coarse graining are described. I then exemplify a class of CG models for proteins, nucleic acids, and lipids, where about 10 non-hydrogen atoms are grouped into one CG particles. Finally, I discuss three sources of speeding up by coarse graining.coarse-grained models / molecular dynamics simulations / biomolecules / Gō models