The GROMOS biomolecular simulation program package
The GROMOS biomolecular simulation program package
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DOI：
10.1021/jp984217f
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发表时间：
1999-05-13
影响因子：
2.9
通讯作者：
van Gunsteren, WF
中科院分区：
文献类型：
--
作者：
Scott, WRP;Hünenberger, PH;van Gunsteren, WF
我们介绍了最新版本的Groningen分子模拟程序包GROMOS96。GROMOS96是为使用分子动力学、随机动力学和能量最小化方法以及路径积分形式对(生物)分子进行动态建模而开发的。对其功能进行了概述，重点介绍了上一个主要版本GROMOS87中未提供的方法。概述了代码的组织，并讨论了设计这个大型(73000行FORTRAN77代码)和复杂程序包所涉及的可靠性、测试和效率问题。最后，我们展示了两个新功能的应用：局部高程模拟和四个空间维度的分子动力学。
We present the newest version of the GROningen MOlecular Simulation program package, GROMOS96. GROMOS96 has been developed for the dynamic modelling of (bio)molecules using the methods of molecular dynamics, stochastic dynamics, and energy minimization as well as the path-integral formalism. An overview of its functionality is given, highlighting methodology not present in the last major release, GROMOS87. The organization of the code is outlined and reliability, testing, and efficiency issues involved in the design of this large (73 000 lines of FORTRAN77 code) and complex package are discussed. Finally, we present two applications illustrating new functionality: local elevation simulation and molecular dynamics in four spatial dimensions.