Simulation project file format

[franknoe]

Define file format for simulation data. A simulation project file should contain:

• a pdb
• metadata (e.g. simulation conditions, program used, force field, etc)
• trajectories

File format should permit:

• addition and removal of trajectories
• extending trajectories, adding and removing frames.
• changing metadata
• efficient read and write operations

Examples:

• hdf5
• compare with MDTraj