VMD

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

Policy

VMD is available to all users of HPC2N.

Citations

Please see the Acknowledging the TCB Group for how to cite VMD etc.

Overview

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.

Usage at HPC2N

On HPC2N we have VMD available as a module.

VMD has been built with the plugins stride and surf.

Loading

To use the VMD module, add it to your environment. You can find versions with 

module spider VMD

and then you can find how to load a specific version (including prerequisites) with

module spider VMD/<version>

Note

Since VMD is a graphical tool, you need to either

  • use ThinLinc (recommended)
  • or log in with 
    ssh -Y username@kebnekaise.hpc2n.umu.se

in order to open the display.

For trajectory files larger than a few GBs, the memory on the login node can be exausted. For such files you can try:

  • preprocess the large trajectory file with MD software built-in tools, for instance, gmx (Gromacs), and cpptraj, (AMBER) to select relevant molecules which can reduce the size of the trajectory. Write the processing instructions in a script that can be run in batch mode in SLURM.
  • preprocess the file with VMD in batch mode through a SLURM batch script. This especially useful for NAMD trajectories.

Additional info