GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
复制标题
DOI：
10.1021/ct700301q
复制
发表时间：
2008-03-01
影响因子：
5.5
通讯作者：
Lindahl, Erik
中科院分区：
文献类型：
--
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
分子模拟是一个非常有用的，但计算非常昂贵的工具，用于研究化学和生物分子系统。在这里，我们展示了我们的分子模拟工具包GROMACS的新实现，它现在既可以通过算法优化和手工编码的例程在单处理器上实现极高的性能，同时也可以在并行机器上很好地扩展。该代码包括最小通信域分解算法、全动态负载平衡、最先进的并行约束求解器和高效的虚拟站点算法，该算法允许去除氢原子自由度，使集成时间步长达到5 fs；对于原子模拟也是并行的。为了提高普通粒子网格Ewald静电算法的缩放特性，我们还使用了多程序，多数据方法，使用单独的节点域负责直接和互反空间相互作用。这种算法组合不仅可以对大型系统进行长时间的模拟，而且还可以在相当少量的标准集群节点上提供模拟性能。
Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs; for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.