VMD

Software name: 
VMD
Policy 

VMD is available to all users of HPC2N.

General 

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.

Description 

VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.

VMD is designed for modeling, 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.

Availability 

On HPC2N we have VMD available as a module on Abisko and Kebnekaise.

VMD has been built with stride and surf.

Usage at HPC2N 

To use the VMD module, first add it to your environment. Use:

module spider vmd

to see which versions are available, as well as how to load the module and the needed prerequisites.

Note that while the case does not matter when you use "ml spider", it is necessary to match the case when loading the modules.

You can read more about loading modules on our Accessing software with Lmod page and our Using modules (Lmod) page.

Note that since VMD is a graphical tool, you need to login with

ssh -Y username@host

in order to open the display.

Additional info 

You can find tutorials and user guides on the VMD homepage.

Updated: 2017-12-06, 15:21