Paper Citing NAMD - Abstract
Mansour, Andrew Abi; Ortoleva, Peter J.
Multiscale Factorization Method for Simulating Mesoscopic Systems with Atomic Precision
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:518-523, FEB 2014
Mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. A multiscale method for simulating these systems in the friction dominated regime from the underlying N-atom formulation is presented. The method integrates notions of multiscale analysis, Trotter factorization, and a hypothesis that the momenta conjugate to coarse-grained variables constitute a stationary process on the time scale of coarse-grained dynamics. The method is demonstrated for lactoferrin, nudaurelia capensis omega virus, and human papillomavirus to assess its accuracy.
