Plumology allows the analysis of biased molecular dynamics data, in particular output from PLUMED. It features:
- Reading plumed output files
- Creating weighted probability distributions, WHAM
- An implementation of a self-organising-map
- Efficient storage and retrieval of data via HDF5
- Wrappers for common backcalculation of experimental values
- Convergence analysis for Metadynamics
- Comparing data from different simulations
- Calculating experimental data RMSDs
- A diverse set of flexible plotting routines
The recommended python distribution is anaconda with python 3.5. Python 2.x is not supported.
Run pip install ./ in the module directory.