Python API

• ufedmm
  • CollectiveVariable
    • CollectiveVariable.effective_mass()
    • CollectiveVariable.evaluate()
  • DynamicalVariable
    • DynamicalVariable.evaluate()
  • ExtendedSpaceContext
    • ExtendedSpaceContext.getState()
    • ExtendedSpaceContext.setPeriodicBoxVectors()
    • ExtendedSpaceContext.setPositions()
    • ExtendedSpaceContext.setVelocitiesToTemperature()
  • ExtendedSpaceSimulation
    • ExtendedSpaceSimulation.add_periodic_task()
    • ExtendedSpaceSimulation.loadCheckpoint()
    • ExtendedSpaceSimulation.saveCheckpoint()
    • ExtendedSpaceSimulation.step()
  • ExtendedSpaceState
    • ExtendedSpaceState.getDynamicalVariables()
    • ExtendedSpaceState.getPositions()
    • ExtendedSpaceState.getVelocities()
  • UnifiedFreeEnergyDynamics
    • UnifiedFreeEnergyDynamics.simulation()
• collective variable package
• analysis
  • Analyzer
    • Analyzer.free_energy_functions()
  • FreeEnergyAnalyzer
    • FreeEnergyAnalyzer.centers_and_mean_forces()
    • FreeEnergyAnalyzer.mean_force_free_energy()
    • FreeEnergyAnalyzer.metadynamics_bias_free_energy()
• integrators
  • AbstractMiddleRespaIntegrator
  • CustomIntegrator
    • CustomIntegrator.step()
  • GeodesicLangevinIntegrator
  • MiddleMassiveGGMTIntegrator
  • MiddleMassiveNHCIntegrator
  • RegulatedNHLIntegrator
  • add_inner_nonbonded_force()
• input/output
  • StateDataReporter
  • Tee
  • deserialize()
  • serialize()
• testmodels
  • AlanineDipeptideModel