PRESTO(PROTEIN ENGINEERING SIMULATOR) - A VECTORIZED MOLECULAR MECHANICS PROGRAM FOR BIOPOLYMERS
PRESTO(PROTEIN ENGINEERING SIMULATOR) - A VECTORIZED MOLECULAR MECHANICS PROGRAM FOR BIOPOLYMERS
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DOI：
10.1016/0097-8485(92)80010-w
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发表时间：
1992-07-01
期刊：
影响因子：
--
通讯作者：
NAKAMURA, H
中科院分区：
文献类型：
--
作者：
MORIKAMI, K;NAKAI, T;NAKAMURA, H
本文介绍了一个高度矢量化的生物高分子分子力学计算程序PRESTO（PRoteinEngineeringSimulaTOr）。PRESTO旨在为许多类型的矢量处理器提供高性能。为了有效地对约束分子动力学模拟进行矢量化，提出了一种新的算法--局部约束算法。在该算法中，完整约束仅限于涉及氢原子的键。在FACOM VP 400 E、Convex C220和Stardent TITAN 3000三种超级计算机上进行了矢量化计算，获得了足够的加速比。
A highly vectorized program for the molecular mechanics computations of biopolymers, PRESTO (PRotein Engineering SimulaTOr) is presented. PRESTO was designed to provide high performance on many types of vector processors. A new algorithm called the localized constraints algorithm was developed in order to vectorize efficiently a constraint molecular dynamics simulation. In this algorithm holonomic constraints were limited to the bonds involving hydrogen atoms. Sufficient speedup was attained by vectorization on three types of supercomputers, the FACOM VP400E, the Convex C220 and the Stardent TITAN3000.