The video shows a diffusion hop of a methane molecule (in turquoise and white) from a large cage to a neighboring large cage in a clathrate hydrate structure of type I (water molecules: red and white).
The trajectory visualized here consists, in fact, of two parts. The first part starts in the middle of the movie (around second 3 to 4), where the methane molecule is located in a narrow window defined by five water molecules. From there, the molecule moves to the left (imagine playing the movie in reverse from the middle). The second part was obtained from the middle in "forward" mode. That is, we reversed the velocities of the atoms in the initial configuration (the one in the middle of the movie) and integrated Newton's equations of motion as usual. Thanks to time reversibility, this is a sound procedure from a theoretical physics point of view. Finally, note that the concatenated trajectories were part of a reactive-flux analysis that we conducted for the associated paper.
The movie was created with CHARMM (trajectory files), VMD (snapshots), and ffmpeg (picture concatenation). My research was supported by the EC through the Marie Curie EXT and EST Projects MEXTCT-2003-023311 and MEST- CT-2005-020491 during this project.