VMD 1.9.1

VMD is designed for modelling, 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 colouring 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 analyse the trajectory of a molecular dynamics (MD) simulation.

Accessing the software

To load the module:

$ module load apps/vmd/v1.9.1

 

VMD should only be run interactively on the large memory logon node, not on a standard logon node. See the help page for running graphical applications for more information.

Use the following command to run VMD:

vmd

 

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

At present there are no previous versions of this application on the BlueBEAR service.

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the VMD website for more information regarding this application.

A VMD tutorial is available on the PMC web site. VMD can download a pdb file directly from the Protein Data Bank by specifying the four-letter code of the protein, for example 1ubq for ubiquitin, in the File Name text entry of the Molecule File Browser window which is opened from the File/New Molecule menu in the VMD Main window and pressing the Load button.

An X server such as Exceed and Exceed3D for Windows are required for the graphical interface. These are available on site license from the Software Sales web site.


Last modified: 8 December 2017