VMD - Visual Molecular Dynamics

VMD (Visual Molecular Dynamics) is a powerful tool for visualizing and analyzing molecular simulations, such as protein, nucleic acid, and lipid systems. It supports a wide range of file formats and integrates with popular molecular dynamics packages like NAMD. VMD offers features for 3D visualization, trajectory analysis, and structure manipulation, making it ideal for researchers in computational biology, biochemistry, and structural biology. It also includes tools for preparing and analyzing systems for simulation.

Check out the documentation for VMD on the Theoretical and Computational Biophysics Group website:

VMD 1.9.3 Documentation (uiuc.edu)

VMD on the cluster

Start an interactive session with a GPU node and --x11 flag:

srun --x11 -p general-gpu -N 1 -n 10 --gres=gpu:1 --pty bash

Check for available versions:

module avail vmd

Load and launch

module load vmd/1.9.4
vmd

Running VMD locally

You can install and run VMD locally on your machine.

Software Downloads (uiuc.edu)

Please don’t hesitate to reach out if you run into any issues with VMD on the cluster.

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Storrs HPC

hpc@storrs.uconn.edu