pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR) method for estimating expectations and free energy differences

Documentation

• Getting started
  • Installing pymbar
  • Running the tests
• Moving from pymbar version 3
  • Snake case
  • More consistent return functionality
  • Simulation output
  • Free energy surfaces
  • Acceleration
  • Other changes
• Strategies for solution
  • Approaches to solving the MBAR equations
  • scipy solvers
  • Built-in solutions
  • Constructing solver protocols
  • Initialization
  • Calculating uncertainties
• The mbar module: MBAR
  • MBAR
• Free energy surfaces with pymbar
  • Free energy surfces
• Other estimators
  • bar()
  • bar_overlap()
  • bar_zero()
  • exp()
  • exp_gauss()
• The timeseries module pymbar.timeseries
  • Automatically identifying the equilibrated production region
  • Subsampling timeseries data
  • Other utility timeseries functions
• Utilities : pymbar.utils
  • BoundsError
  • ConvergenceError
  • DataError
  • ParameterError
  • TypeCastPerformanceWarning
  • check_w_normalized()
  • ensure_type()
  • kln_to_kn()
  • kn_to_n()
  • logsumexp()
• Bibliography

Indices and tables

• Index

• Module Index

• Search Page