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VMD

Making a Movie from a Trajectory

Step 1

The required files to create a movie for VMD analysis are the parameter/topology file (.prmtop), the experimental trajectory (.trj or mdcrd), and the script with presets we have found useful to visualize our system (.sh). The visualization script will need to be modified to point to the correct prmtop and trajectory files. Then, open VMD.

Step 2

Three windows will pop up: a display window, a main menu window, and a terminal window. In the terminal window next to the vmd > prompt, type "play (path_to_script)/(script_name).sh." After a few seconds, the customized view of the trajectory should appear in the display window.

Step 3

Play the trajectory and adjust the view/representations in order to achieve the desired view for the movie to be made. It is helpful to switch between modes -- hit R on the keyboard for rotation mode, T on the keyboard for translocation mode, and S on the keyboard for scale mode -- and then adjust with the mouse. If you would like to save a script using the current view as the presets type "save_state (path_to_script)/(script_name).sh."

Step 4

To export the frames of the movie, go to the main menu window > Extensions > Visualization > Movie Maker. The VMD Movie Generator window will open. Change the working directory to where you would like the files to go. Then under Movie Settings, select Trajectory as the movie type and uncheck Delete image files. Then click Make Movie. If prompted to specify a path to VideoMach, click No and ignore the warning. The video frames should have appeared in your specified working directory.

Step 5

Stitch the movie frames together using the video editing software of your choice. iMovie (Mac) and lightworks (PC) are free and have worked well so far.

Note: There is a video tutorial available showing the complete process of making a movie from a trajectory.