Resolution exchange simulation

被引:166
作者
Lyman, E
Ytreberg, FM
Zuckerman, DM
机构
[1] Univ Pittsburgh, Dept Computat Biol, Sch Med, Pittsburgh, PA 15213 USA
[2] Univ Pittsburgh, Dept Environm & Occupat Hlth, Grad Sch Publ Hlth, Pittsburgh, PA 15213 USA
关键词
D O I
10.1103/PhysRevLett.96.028105
中图分类号
O4 [物理学];
学科分类号
0702 [物理学];
摘要
We extend replica-exchange simulation in two ways and apply our approaches to biomolecules. The first generalization permits exchange simulation between models of differing resolution-i.e., between detailed and coarse-grained models. Such "resolution exchange" can be applied to molecular systems or spin systems. The second extension is to "pseudoexchange" simulations, which require little CPU usage for most levels of the exchange ladder and also substantially reduce the need for overlap between levels. Pseudoexchanges can be used in either replica or resolution exchange simulations. We perform efficient, converged simulations of a 50-atom peptide to illustrate the new approaches.
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页数:4
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