Modeling real dynamics in the coarse-grained representation of condensed phase systems.
This work presents a systematic multiscale methodology to provide a more faithful representation of real dynamics in coarse-grained molecular simulation models. The theoretical formalism is based on the recently developed multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B. 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] and relies on the generalized Langevin equation approach and its simpler Langevin equation limit. The friction coefficients are determined in multiscale fashion from the underlying all-atom molecular dynamics simulations using force-velocity and velocity-velocity correlation functions for the coarse-grained sites. The diffusion properties in the resulting CG Brownian dynamics simulations are shown to be quite accurate. The time dependence of the velocity autocorrelation function is also well-reproduced relative to the all-atom model if sufficient resolution of the CG sites is implemented.
Izvekov
Sergei
S
Center for Biophysical Modeling and Simulation and Department of Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.
Voth
Gregory A
GA
D003198:Computer Simulation; D004058:Diffusion; D008956:Models, Chemical; D044367:Phase Transition; D011789:Quantum Theory