粗粒化系统的GROMACS模拟  

Simulation of coarse-grained system using GROMACS

作　　者：冯剑[1] Feng Jian

机构地区：[1]滁州学院材料与化学工程学院

出　　处：《滁州学院学报》2018年第5期24-28,共5页Journal of Chuzhou University

基　　金：国家自然科学基金(21476072)

摘　　要：GROMACS是一款被广泛采用的分子动力学模拟软件。本文从扩展力场出发,使之适用于粗粒化系统的模拟,从而能使用GROMACS标准工具生成拓扑,构建分子系统。同时使用粗粒化的MARTINI势能对两个分子系统进行模拟和验证。最后给出了GROMACS单位到更一般粗粒化系统的映射方法。本文采用的方法对将GROMACS扩展到实际的非生物分子体系也有重要的借鉴作用。GROMACS is a widely used molecular dynamics simulation software.In this paper,a force field is extended to apply for the simulation of coarse-grained system,so that the topology can be generated and the molecular system can be constructed by using GROMACS standard tools.At the same time,two molecular systems were simulated and verified using the coarse-grained MARTINI potential energy.Finally,the mapping method of GROMACS units to more general coarse-grained system is given.The method used in this paper can also be used as a reference for the extension of GROMACS to actual non-biomolecular systems.

关 键 词：分子动力学模拟 粗粒化 力场 GROMACS 

分 类 号：O642.5[理学—物理化学]