Visual Molecular Dynamics (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

Open OnDemand

Select VMD from the Interactive Apps dropdown.

Enter the walltime and select the partition to run VMD. Click "Launch" to submit your request to the SLURM scheduler.

When resources are available, a blue "Launch Visualization" button will appear. Click the button to launch VMD.

VMD on Open OnDemand

Useful Links

http://www.ks.uiuc.edu/Research/vmd/

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