VMD: Difference between revisions
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ppmtompeg [http://netpbm.sourceforge.net/ Netpbm Package Website] | ppmtompeg included in [http://netpbm.sourceforge.net/ Netpbm Package Website] | ||
'''WINDOWS''' | '''WINDOWS''' | ||
Revision as of 13:58, 1 June 2007
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. VMD Download 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
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. VMD Plugins Download 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
Create Movies with VMD
Additional Software Required To Create Movies
LINUX ppmtompeg included in Netpbm Package Website
WINDOWS VideoMach 4.0.4. VideoMach Website We don't have a licence for this software, but there is a 30 days trial version.
Additional Software Required To Create High Definition Images
LINUX & WINDOWS POV-Ray 3.6. POV-Ray Website
VMD Images and Movies Tutorial