Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden.
Bioinformatics. 2013 Apr 1;29(7):845-54. doi: 10.1093/bioinformatics/btt055. Epub 2013 Feb 13.
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.
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.
GROMACS is an open source and free software available from http://www.gromacs.org.
Supplementary data are available at Bioinformatics online.
分子模拟在历史上一直是一种低通量技术，但更快的计算机和越来越多的基因组和结构数据正在通过启用大规模自动化模拟，例如，具有或不具有一系列配体的生物分子的许多构象或突变体，从而改变这种情况。与此同时，性能和扩展方面的进步现在使得可以直接通过实验测试复杂的生物分子相互作用和功能的建模。这些应用都需要快速有效的软件，可以在集群、Web 服务器、分布式计算或云资源上大规模部署。
在这里，我们展示了在过去 4 年中开发的一系列新的模拟算法和功能，这些功能最终形成了 GROMACS 4.5 软件包。该软件现在可以自动处理广泛的生物分子类别，如蛋白质、核酸和脂质，并内置了这些分子常用的所有力场。GROMACS 支持几种隐式溶剂模型以及新的自由能算法，并且该软件现在使用多线程进行高效并行化，即使在低端系统（包括基于 Windows 的工作站）上也是如此。与手工调优的装配内核和最先进的并行化相结合，这为高通量以及大规模并行模拟提供了极高的性能和成本效益。
GROMACS 是一个开源免费软件，可从 http://www.gromacs.org 获得。
补充数据可在 Bioinformatics 在线获得。
