A fast script to wrap atoms or molecules into a simulation box using MDTraj as a backend.
Use the bash command wrap_traj
-f unwrapped trajectory file (must be a MDTraj supported file format)
-c topology file (must be a MDTraj supported file format)
-o output file (must be a MDTraj supported file format)
--nowhole [don't] keep molecules whole
--center center the box at the origin