VMD: Visual molecular dynamics
VMD: Visual molecular dynamics
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DOI：
10.1016/0263-7855(96)00018-5
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发表时间：
1996-02-01
影响因子：
2.9
通讯作者：
Schulten, K
中科院分区：
文献类型：
--
作者：
Humphrey, W;Dalke, A;Schulten, K
VMD是一个分子图形程序，旨在显示和分析分子组件，特别是生物聚合物，例如蛋白质和核酸。 VMD可以使用多种渲染样式和着色方法同时显示任何数量的结构。分子显示为一个或多个“表示”，其中每个表示形式体现了所选原子子集的特定渲染方法和着色方案。使用广泛的原子选择语法选择每个表示中显示的原子，其中包括布尔操作员和正则表达式。 VMD提供了一个完整的图形用户界面，用于程序控制，以及使用TCL嵌入式解析器的文本界面，以允许具有可变替换，控制循环和功能调用的复杂脚本。支持完整的会话记录，该记录将生成一个VMD命令脚本以供以后播放。显示的分子的高分辨率栅格图像可以通过生成输入脚本来生成供许多逼真的图像渲染应用程序使用。 VMD还具有明确设计的，具有动画分子动力学（MD）模拟轨迹的能力，该轨迹是从文件或直接连接到运行的MD模拟的。 VMD是MDSCOPE的可视化组件，MDSCOPE是结构生物学中的一组用于交互式问题的工具，其中还包括并行MD程序NAMD以及用于连接可视化和仿真程序的MDCOMM软件。 VMD使用面向对象的设计编写C ++；该程序（包括源代码和广泛的文档）可以通过匿名FTP和万维网免费获得。
VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more ''representations,'' in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.