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VMD visualization
VMD is an interactive atomic and molecular graphics program suited for the visualization of simple atoms/molecules to more complicated structures like proteins, nucleic acids, lipids, and membranes. Some of its many features include viewing molecular dynamics trajectories, optimizations and charge distributions. It supports a variety of atomic/molecular formats. Please see the following website below for details and the user guide.
VMD homepage
The authors request that any published work or images created using VMD include the following reference at a minimum; please refer to VMD's Homepage for full reference in various formats: Humphrey, W., Dalke, A. and Schulten, K., "VMD - Visual Molecular Dynamics" J. Molec. Graphics 1996, 14.1, 33-38.
To make use of VMD remember to enable X11 forwarding. It is recommended to install VMD locally for improved performance, and less load on the cluster head. Refer to the VMD homepage to learn how you can obtain the software for personal use.
$ module load vmd
$ vmd