在 AMBER 中快速实现 Nudged Elastic Band 方法。
Fast Implementation of the Nudged Elastic Band Method in AMBER.
机构信息
Department of Physics , University of Florida , Gainesville , Florida 32611 , United States.
Laboratory for Biomolecular Simulation Research, Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854 , United States.
出版信息
J Chem Theory Comput. 2019 Aug 13;15(8):4699-4707. doi: 10.1021/acs.jctc.9b00329. Epub 2019 Jul 31.
Abstract
We present a fast implementation of the nudged elastic band (NEB) method into the particle mesh Ewald molecular dynamics module of the Amber software package for both central processing units (CPU) and graphics processing units (GPU). The accuracy of the new implementation has been validated for three cases: a conformational change of alanine dipeptide, the α-helix to β-sheet transition in polyalanine, and a large conformational transition in the human 8-oxoguanine-DNA glycosylase with DNA complex (OGG1-DNA). Timing benchmark tests were performed on the explicitly solvated OGG1-DNA system containing ∼50 000 atoms. The GPU-optimized implementation of NEB achieves a more than two orders of magnitude speedup compared with the previous CPU implementation performed with a two-core CPU processor. The speed and scalable features of this implementation will enable NEB applications on larger and more complex systems.
摘要
我们在 Amber 软件包的粒子网格 Ewald 分子动力学模块中引入了一种快速的 Nudged Elastic Band (NEB) 方法的实现，适用于中央处理器 (CPU) 和图形处理单元 (GPU)。新实现的准确性已经通过三种情况进行了验证：丙氨酸二肽的构象变化、多丙氨酸中的α-螺旋到β-折叠转变，以及与人 8-氧鸟嘌呤-DNA 糖基化酶与 DNA 复合物 (OGG1-DNA) 的大构象转变。在含有约 50000 个原子的明胶溶剂 OGG1-DNA 系统上进行了定时基准测试。与使用双核 CPU 处理器执行的先前 CPU 实现相比，GPU 优化的 NEB 实现实现了超过两个数量级的速度提升。这种实现的速度和可扩展性将使更大和更复杂系统上的 NEB 应用成为可能。
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