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choderalab / saltswap

Package to fluctuate the number of counterions in an OpenMM simulation
MIT License
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New data storage tool #7

Closed gregoryross closed 7 years ago

gregoryross commented 7 years ago

Created a new netcdf storage module for a stable way to record saltswap simulation data. The previous way of storing results used text files with custom write-read functions. Basing the storage system on netcdf with a unit-tested interface is a more sustainable option.

gregoryross commented 7 years ago

Does this actually run?

Yes, my unit tests (in test_recorder.py) test the reading and writing of simulation data

And where do you store the configurations sampled?

I'll be storing the simulation configurations with dcd files as this makes it easiest to view the simulations.

jchodera commented 7 years ago

Yes, my unit tests (in test_recorder.py) test the reading and writing of simulation data

Great! I was worried the zlib argument to Dataset might cause problems since it wasn't listed in the docs.

I'll be storing the simulation configurations with dcd files as this makes it easiest to view the simulations.

XTC or DCD should be fine.