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Plumology - Tools to analyse biased molecular dynamics simulations

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Plumology

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

Dependencies

The recommended python distribution is anaconda with python 3.5. Python 2.x is not supported.

Install

Run pip install ./ in the module directory.

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Plumology - Tools to analyse biased molecular dynamics simulations

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