VMD软件使用指南.PDFVIP

VMD 软件使用指南 2009 年7 月 中国科学院计算机网络信息中心超级计算中心 1 目录 Tinker 软件使用指南1 目录2 1. 软件介绍3 2. 软件的安装与测试3 安装方法3 2.1 安装目录及安装信息 3 2.2 测试结果 3 3. 软件的运行使用方法6 2 1. 软件介绍 VMD 是分子可视化程序，使用OpenGL 提供高质量的3D 分子图形。用于显示、动画 演示和分析大的生物分子体系。 VMD is designed for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. It may be used to view more general molecules, as VMD can read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides a wide variety of methods for rendering and coloring a molecule: simple points and lines, CPK spheres and cylinders, licorice bonds, backbone tubes and ribbons, cartoon drawings, and others. VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. 2. 软件的安装与测试 安装方法 下载：/Development/Download/download.cgi?PackageName=VMD 选择“LINUX_64 OpenGL, CUDA ”版（需要注册） 解压vmd-1.8.7beta5.bin.LINUXAMD64.opengl.tar.gz 进入解压目录，编辑configure ： $install_bin_dir=/home_soft/soft/x86_64/apps/OpenSoft/vmd/vmd-1.8.7beta5/bin; $install_library_dir=/home_soft/soft/x86_64/apps/OpenSoft/vmd/vmd-1.8.7beta5/lib/$instal l_name; 生成makefile ： ./configure 安装： make install 2.1 安装目录及安装信息 源代码位置: /home_soft/soft/x86_64/apps/OpenSoft/vmd/vmd-src/ 安装后可运成程序的目录为：/home_soft/soft/x86_64/apps/