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
CIRCEaccount holders
Platforms
CIRCEcluster
Running VMD on the Cluster
Starting the Application
Before you login to CIRCE, you need to make sure you have X11 Forwarding enabled. If you’re logging in from a UNIX/Linux system, you will need to do the following:
ssh -Y user@circe.rc.usf.edu
To run VMD, simply execute the following within your job directory:
[user@host ~]$ module add apps/vmd [user@host ~]$ vmd
For Windows, Mac, and Linux users, VMD can also be launched through the CIRCE Desktop Environment using the Applications menu. For more information about the CIRCE Desktop Environment, please see our CIRCE Desktop Environment documentation.
Additional Documentation
- VMD Documentation
- http://www.ks.uiuc.edu/Research/vmd/current/docs.html
Reporting Bugs
Report bugs with VMD to the IT Help Desk: rc-help@usf.edu