Requirements: interoperability

[avirshup]

The file format should support common input and output for these applications:

At minimum:

1. Molecular dynamics: simulation (OpenMM, DESMOND, etc.) and analysis packages (MDTraj, PyTraj, etc.)
2. Quantum chemistry (PySCF, Psi4, NWChem, GAMESS, etc.)
3. Docking (UCSF-, Auto-, GLIDE, etc.)
4. Informatics (OpenBabel, RDKit, OEChem, etc.) - see Requirements: Chemoinformatics #9

With the ability to support these in the future, either as part of the standard or with domain-specific extensions:

1. Excited state dynamics: Surface hopping, AIMS, MCTDH, etc.
2. Coarse grained simulations: MARTINI, rigid body MD, etc.
3. Visualization (colors, annotations, representations, etc. for VMD, Chimera, etc.)

[egonw]

That means, link any term you use in the format to an ontology.