GROMACS - A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION
GROMACS - A MESSAGE-PASSING PARALLEL MOLECULAR-DYNAMICS IMPLEMENTATION
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DOI：
10.1016/0010-4655(95)00042-e
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发表时间：
1995-09-01
影响因子：
6.3
通讯作者：
VANDRUNEN, R
中科院分区：
文献类型：
--
作者：
BERENDSEN, HJC;VANDERSPOEL, D;VANDRUNEN, R
介绍了一种适用于水环境中生物（大）分子的分子动力学（MD）程序的并行消息传递实现。该软件是为定制设计的32处理器环GROMACS（GROningen MAchine for Chemical Simulation）开发的，可以与左右邻居进行通信，但可以在任何并行系统上运行，可以将处理器环映射到该系统上，并支持类似于PVM的块发送和接收调用。GROMACS软件由一个预处理器、一个并行MD和能量最小化程序组成，该程序可以使用任意数量的处理器（包括一个）、一个可选的监视器和几个分析工具。这些程序是用ANSI C编写的，可通过FTP获得（信息：chem.rug.nl）。该功能基于GROMOS（GROningen Molecular Simulation）包（货车Gunsteren和Berendsen，1987; BIOMOS B. V.，Nijenborgh 4，9747 AG Groningen）。包括GROMOS和GROMACS格式之间的转换程序。MD程序可以处理温度和压力定标的矩形周期边界条件。可以不修改地处理的相互作用是具有库仑势和Lennard-Jones势或Buckingham势的可变非键对相互作用，使用基于电荷群的双程截止，以及键和键角的谐波或约束类型的固定键相互作用和二面角的周期或余弦幂级数相互作用，特殊的力可以添加到粒子组（用于非平衡动力学或位置约束）或粒子之间（用于距离约束）。并行性是基于粒子分解。处理器间的通信很大程度上限于每个时间步长一次的环上的位置和力分布。
A parallel message-passing implementation of a molecular dynamics (MD) program that is useful for bio(macro) molecules in aqueous environment is described. The software has been developed for a custom-designed 32-processor ring GROMACS (GROningen MAchine for Chemical Simulation) with communication to and from left and right neighbours, but can run on any parallel system onto which a a ring of processors can be mapped and which supports PVM-like block send and receive calls. The GROMACS software consists of a preprocessor, a parallel MD and energy minimization program that can use an arbitrary number of processors (including one), an optional monitor, and several analysis tools. The programs are written in ANSI C and available by ftp (information: gromacs @chem.rug.nl). The functionality is based on the GROMOS (GROningen Molecular Simulation) package (van Gunsteren and Berendsen, 1987; BIOMOS B.V., Nijenborgh 4, 9747 AG Groningen). Conversion programs between GROMOS and GROMACS formats are included.The MD program can handle rectangular periodic boundary conditions with temperature and pressure scaling, The interactions that can be handled without modification are variable non-bonded pair interactions with Coulomb and Lennard-Jones or Buckingham potentials, using a twin-range cut-off based on charge groups, and fixed bonded interactions of either harmonic or constraint type for bonds and bond angles and either periodic or cosine power series interactions for dihedral angles, Special forces can be added to groups of particles (for non-equilibrium dynamics or for position restraining) or between particles (for distance restraints). The parallelism is based on particle decomposition. Interprocessor communication is largely limited to position and force distribution over the ring once per time step.