set a VERSION key in the hdf5 files that can be incremented when the format needs to change about mdtraj HOT 4 CLOSED

This is a great idea. I think we might also want to come up with a "formal" standard for our HDF5 format. Just a document that describes everything, the keys, how we handle future versions. Then we could pass it around to some of the MSMBuilder list to see what they think. The idea is to make something foolproof for the future.

I also think PyTables is so fast that this could be a game-changer for a lot of applications.

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Yeah, good idea.

Having some pytables/hdf5 performance benchmarks vs. dcd or xtc might not be a bad idea.

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So here's another random idea: make it trivial to use our HDF5 format for trajectory output and system serialization in OpenMM.

It would be great if we could simply "resume" an arbitrary trajectory for more sampling. I wonder if this sort of feature could be useful for MSM Accelerator. When you need to start new sampling, you just grab the frame of interest and go.

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The version key is part of the new HDF5 format.

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