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Visualization Software

VMD Tutorials

Download VMD and Manual
To download VMD and the documentation, please see the VMD website. Please note that VMD no longer supports OpenGL and therefore does not work on MacOSX from Catalina and newer (10.15 and on).

Using VMD with AMBER
This tutorial acts as a brief introduction to using VMD for visualising AMBER inpcrd, restrt and trajectory files. While only scratching the surface of what VMD can do it covers setting up a .vmdrc file to set the default layout of VMD, loading static structures and performing RMSD fits between similar structures. It then goes on to cover loading and visualising AMBER trajectories, both from gas phase/implicit solvent simulations and from periodic boundary simulations and shows how to save individual frames from a trajectory as well as create an MPEG video of the trajectory. By Ross Walker.

VMD Movie Making
This is a tutorial on how to make an mp4 movie in VMD from your Amber trajectory. By Rodrigo Galindo-Murillo.

Official VMD Tutorials
VMD makes their own tutorials, which are also helpful.

Chimera Tutorials

Download Chimera-X and Manual
This is the link to download Chimera-X a visualization program from UCSF.

"How's that for maxed out?"

Last modified: Oct 26, 2023