VMD

Description

From the VMD website: 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.

Version

  • 1.9

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

VMD requires the following module file to run:

  • apps/vmd/1.9

Running VMD on CIRCE/SC

The VMD user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Starting the Application

Establishing a GUI connection to CIRCE/SC

To use VMD, you will need to connect to CIRCE/SC with GUI redirection, either using:

  • CIRCE/SC Desktop Environment
  • SSH with X11 redirection
    • If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
      • [user@localhost ~]$ ssh -X circe.rc.usf.edu
        or
      • [user@localhost ~]$ ssh -X sc.rc.usf.edu

Once connected to CIRCE/SC, you can open VMD using the steps below:

[user@login0 ~]$ module add apps/vmd/1.9
[user@login0 ~]$ vmd

Documentation

Home Page, User Guides, and Manuals

Reporting Bugs

Report bugs with VMD to the IT Help Desk: rc-help@usf.edu