GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
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DOI：
10.1093/bioinformatics/btt055
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发表时间：
2013-04-01
期刊：
影响因子：
5.8
通讯作者：
Lindahl, Erik
中科院分区：
文献类型：
--
作者：
Pronk, Sander;Pall, Szilard;Lindahl, Erik
动机：分子模拟在历史上一直是一种低通量的技术，但更快的计算机和越来越多的基因组和结构数据正在改变这一点，例如，通过大规模自动模拟许多构象异构体或生物分子的突变体，有或没有一系列配体。与此同时，性能和规模的进步现在使得以可通过实验直接测试的方式模拟复杂的生物分子相互作用和功能成为可能。这些应用程序都需要快速高效的软件，可以大规模部署在集群，Web服务器，分布式计算或云资源。结果：在这里，我们提出了一系列新的模拟算法和功能，在过去的4年中开发，导致GROMACS 4.5软件包。该软件现在可以自动处理各种生物分子，如蛋白质、核酸和脂质，并内置了这些分子的所有常用力场。GROMACS支持几种隐式溶剂模型，以及新的自由能算法，该软件现在使用多线程进行高效并行化，即使在低端系统上，包括基于Windows的工作站。结合手动调整的汇编内核和最先进的并行化，这为高吞吐量和大规模并行模拟提供了极高的性能和成本效益。
Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources.Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.