Paper Citing NAMD - Abstract
Ortoleva, P.; Singharoy, A.; Pankavich, S.
Hierarchical multiscale modeling of macromolecules and their assemblies
SOFT MATTER, 9:4319-4335, 2013
Soft materials (e. g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character of such systems often makes traditional molecular dynamics simulation impractical, a multiscale approach has been presented that allows for long-time simulation with atomic detail based on the co-evolution of slowly varying order parameters (OPs) with the quasi-equilibrium probability density of atomic configurations. However, this approach breaks down when the structural change is extreme, e. g., when nearest-neighbor connectivity between structural subsystems is not maintained. In the current study, a self-consistent approach is presented wherein OPs and a reference structure co-evolve slowly to yield long-time simulation for dynamical soft-matter phenomena such as structural transitions and self-assembly. The development begins with the Liouville equation for N classical atoms and an ansatz on the form of the associated N-atom probability density. Multiscale techniques are used to derive Langevin equations for the coupled OP-configurational dynamics. The net result is a set of equations for the coupled stochastic dynamics of the OPs and centers of mass of the subsystems that constitute a soft material body. The theory is based on an all-atom methodology and an interatomic force field, and therefore enables calibration-free simulations of soft matter, such as macromolecular assemblies.
