Paper Citing NAMD - Abstract
Yang, J.; Singharoy, A.; Sereda, Yu. V.; Ortoleva, P. J.
Quasiequivalence of multiscale coevolution and ensemble MD simulations: A demonstration with lactoferrin
CHEMICAL PHYSICS LETTERS, 616:154-160, NOV 25 2014
Ensemble molecular dynamics computations are performed because a single MD simulation may not represent all the possible scenarios. Ensemble MD consumes a great amount of resources. Here, the similarity of ensemble MD and coupled all-atom, coarse-grained simulation (the multiscale coevolution method) is assessed. Quasiequivalence of two simulations is defined and shown to provide a similarity measure. Quasiequivalence compares trajectories on coarse and relatively finer scales. Good agreement between multiscale coevolution and ensemble MD simulations is demonstrated for lactoferrin. Quasiequivalence along with greater CPU efficiencies of multiscale coevolution relative to ensemble MD, underscore the advantages of multiscale coevolution for nanosystem modeling. (C) 2014 Elsevier B.V. All rights reserved.
