TY - JOUR
T1 - Quasiequivalence of multiscale coevolution and ensemble MD simulations
T2 - A demonstration with lactoferrin
AU - Yang, J.
AU - Singharoy, A.
AU - Sereda, Yu V.
AU - Ortoleva, P. J.
N1 - Publisher Copyright:
© 2014 Published by Elsevier B.V.
PY - 2014/11/25
Y1 - 2014/11/25
N2 - 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.
AB - 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.
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U2 - 10.1016/j.cplett.2014.10.020
DO - 10.1016/j.cplett.2014.10.020
M3 - Article
AN - SCOPUS:84908457672
SN - 0009-2614
VL - 616-617
SP - 154
EP - 160
JO - Chemical Physics Letters
JF - Chemical Physics Letters
ER -