VMD is available to all users of HPC2N.
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
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.
On HPC2N we have VMD available as a module on Abisko and Kebnekaise.
VMD has been built with stride and surf.
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.
Note that since VMD is a graphical tool, you need to login with
ssh -Y username@host
in order to open the display.
You can find tutorials and user guides on the VMD homepage.