I have so far been using VMD to create visualizations of molecular trajectories. However, I find myself not entirely satisfied with the quality of the resulting animations—when you want to do snapshot-by-snapshot movies, the simulation "moves" too quickly.

Additionally, I sometimes receive individual graphics images, and need to convert those into an animation. Since I worked on OS X, I've tried both imageMagick and more recently the built-in iMovie. However, I'd like more flexibility in the available movie formats than imageMagick provides, and more command-line interface control than iMovie offers.

So, what I'd like to know is, are there other visualization tools that can either:

  • given a MD trajectory, can produce the snapshots and an animation of the complete trajectory with more control provided than VMD; or
  • given a set of snapshots (in TGA, TIFF, PNG, etc.), can produce animations in multiple formats (MPEG, M4V, etc.)?
  • $\begingroup$ For a similar, but not duplicate, question, see scicomp.stackexchange.com/questions/898/…. $\endgroup$ – Geoff Oxberry Feb 17 '12 at 19:11
  • $\begingroup$ Hi aeismail, I just thought I'd let you know that Chemistry.SE has launched into public beta, and has a nice core of molecular simulation users… $\endgroup$ – F'x May 9 '12 at 10:08

I like to use ffmpeg for movies from stills. I found this to be better than imovie and imageMagick. Just makes sure on the mac you grab the right codecs (don't remember off hand which I needed to get things working) and restart your computer after install them. Also, ffmpeg is available on macports if that's your thing.

Don't know much about molecular dynamics visulization, but you could look into VisIT. It has some molecular dynamics support according to the FAQ, and the developers are pretty responsive and helpful if you need that.

  • $\begingroup$ +1, Based on the Wikipedia page listing the output formats supported (presumably with the appropriate codecs installed), this answer appears to answer the second question well. (Don't know about answering the first one, because I know nothing about MD.) $\endgroup$ – Geoff Oxberry Feb 17 '12 at 19:15

If you want to become a real movie star, you should check: http://www.molecularmovies.com/

For the snapshots thing you can play with mpeg encoder


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