Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations
Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations
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DOI：
10.1021/ct400727q
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发表时间：
2014-01-01
影响因子：
5.5
通讯作者：
Voth, Gregory A.
中科院分区：
文献类型：
--
作者：
Grime, John. M. A.;Voth, Gregory A.
The use of coarse-grained (CG) models can significantly increase the time and length scales accessible to computational molecular dynamics (MD) simulations. To address very large-scale phenomena, however, requires a careful consideration of memory requirements and parallel MD load balancing in order to make efficient use of current supercomputers. In this work, a CG-MD code is introduced which is specifically designed for very large, highly parallel simulations of systems with markedly non-uniform particle distributions, such as those found in highly CG models having an implicit solvent. The CG-MD code uses an unorthodox combination of sparse data representations with a Hilbert space-filling curve (SFC) to provide dynamic topological descriptions, reduced memory overhead, and advanced load-balancing characteristics. The results of representative large-scale simulations indicate that our approach can offer significant advantages over conventional MD techniques, and should enable new classes of CG-MD systems to be investigated.
