Hsin Jen, Arkhipov Anton, Yin Ying, Stone John E, Schulten Klaus
Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Curr Protoc Bioinformatics. 2008 Dec;Chapter 5:Unit 5.7. doi: 10.1002/0471250953.bi0507s24.
VMD (Visual Molecular Dynamics) is a molecular visualization and analysis program designed for biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. This unit will serve as an introductory VMD tutorial. We will present several step-by-step examples of some of VMD's most popular features, including visualizing molecules in three dimensions with different drawing and coloring methods, rendering publication-quality figures, animating and analyzing the trajectory of a molecular dynamics simulation, scripting in the text-based Tcl/Tk interface, and analyzing both sequence and structure data for proteins.
VMD（可视化分子动力学）是一款为蛋白质、核酸、脂质双层组装体等生物系统设计的分子可视化与分析程序。本单元将作为VMD的入门教程。我们将给出一些VMD最常用功能的逐步示例，包括使用不同的绘制和着色方法对分子进行三维可视化、渲染高质量的发表级图形、对分子动力学模拟轨迹进行动画制作与分析、在基于文本的Tcl/Tk界面中编写脚本，以及分析蛋白质的序列和结构数据。
