Van Der Spoel David, Lindahl Erik, Hess Berk, Groenhof Gerrit, Mark Alan E, Berendsen Herman J C
Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden.
J Comput Chem. 2005 Dec;26(16):1701-18. doi: 10.1002/jcc.20291.
This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.
本文介绍了GROMACS软件套件（格罗宁根化学模拟机器），它于20世纪90年代初由荷兰格罗宁根大学开发。该软件用ANSI C编写，源自一个并行硬件项目，非常适合在处理器集群上进行并行化。通过对邻居搜索和内循环性能的精心优化，GROMACS是一个用于分子动力学模拟的非常快速的程序。它没有自己的力场，但与GROMOS、OPLS、AMBER和ENCAD力场兼容。此外，它可以处理可极化壳模型和灵活约束。该程序用途广泛，因为用户可以添加力例程、指定列表函数，并且可以轻松定制分析。纳入了非平衡动力学和自由能测定。提供了与流行量子化学软件包（MOPAC、GAMES-UK、GAUSSIAN）的接口，以执行混合MM/QM模拟。该软件包包括约100个实用程序和分析程序。GROMACS属于公共领域，根据GNU通用公共许可证进行分发（包括源代码和文档）。它由来自格罗宁根大学、乌普萨拉大学和斯德哥尔摩大学以及美因茨马克斯·普朗克聚合物研究所的一组开发人员维护。其网站是http://www.gromacs.org。
