VMD

VMD is designed for the 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.

How Install VMD in your Desktop PC

Download the latest version (1.8.6.) from VMD Website.

LINUX
VMD for LINUX OpenGL (Linux (Redhat 9 or later) with Mesa or hardware OpenGL)

Unzip and untar the file in ./home/username/VMD/

Run VMD using vmd_LINUX executable. It is in ./home/username/VMD/LINUX/vmd_LINUX

WINDOWS 
VMD for Windows OpenGL (Microsoft Windows 2000/XP/Vista (32-bit) using OpenGL)
 
Install MSI file using Windows Installer

Run VMD 

Installation Guide

Environment Variables

LINUX
VMDDIR : The directory which contains the VMD data files (such as this help file) and 
architecture-specific executables. By default, this is /usr/local/lib/vmd on Unix systems.

VMDTMPDIR : The directory which VMD should use for temporary data files. By default, this
is /tmp, or /usr/tmp on Unix systems. 

LD_LIBARY_PATH : On Unix systems add /usr/lib

Update Plugins

Download the latest plugins release (1.8.5) from VMD Website.

LINUX
Unzip and untar the file in ./home/username/VMD/plugins/

WINDOWS 
Unzip the file in C:\Archivos de programa\University of Illinois\VMD\plugins\

VMD Tutorial

VMD Tutorial

Create Movies with VMD

VMD Images and Movies Tutorial

Links

Visual Molecular Dynamics Website