Truncate Trajectory (VMD plugin)

Large trajectories have a lot of redundant hetero compounds which augment their size and render calculations cumbersome. Truncate Trajectory is designed to help you discard these compounds. It currently works only with parallelepiped unit cells and periodic boundary conditions, as it is able to detect periodic contacts with hetero compounds from the 26 nearest cells, and incorporates these compounds to the final trajectory. The dimensions and angles (a, b, c, alpha, beta, and gamma) should be also provided in the original trajectory files (if not please contact me: tevang3@gmail.com).

In the current version you can define how many water molecules to keep but not other hetero compounds. If you want to keep other hetero compounds (e.g. ions, ligands, etc.) then you will have to keep ALL of them. In future versions you will be able to specify how many non-water hetero compounds to keep (development is under way).