Paper Citing NAMD - Abstract
Miao, Yinglong; Ortoleva, Peter J.
Viral Structural Transition Mechanisms Revealed by Multiscale Molecular Dynamics/Order Parameter eXtrapolation Simulation
BIOPOLYMERS, 93:61-73, JAN 2010
On the basis of an all-atom multiscale analysis theory of nanosystem dynamics, a multiscale molecular dynamics/order parameter extrapolation (MD/OPX) approach has recently been developed. It accelerates MD for long-time simulation of large bionanosystems and addresses rapid atomistic fluctuations and slowly varying coherent dynamics simultaneously. In this study, MD/OPX is optimized and implemented to simulate viral capsid structural transitions. Specifically, 200 ns MD/OPX simulation of the swollen state of cowpea chlorotic mottle virus capsid reveals that it undergoes significant energy-driven shrinkage in vacuum, which is a symmetry-breaking process involving local initiation and front propagation. (C) 2009 Wiley Periodicals, Inc. Biopolymers 93:61-73, 2010.
