sandbox's People
sandbox's Issues
Reorganize Analysis Chapter
Split Analysis subsections into largely independent chapters
Reorganize analysis
Split analysis subsections into largely independent chapters
Simulation project file format
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
Hierarchical TICA
Implement simulation project file format
Implement in stallone
Implement hierarchical TICA
Put hierarchical TICA into code
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