molecular_simulations.simulate.constantph.reference_energy module

class molecular_simulations.simulate.constantph.reference_energy.ReferenceEnergyFinder(model, pKa, temperature)[source]

Bases: object

Construct a ReferenceEnergyFinder.

Parameters:

  • model (ConstantPH) – The model for which to determine reference energies. It must contain a single titratable residue with exactly two states. It does not matter what pH or reference energies were specified when it was created, because they will both be overwritten.

  • pKa (float) – The experimental pKa of the titratable residue. Reference energies will be chosen to match it.

  • temperature (openmm.unit.Quantity) – The temperature at which the simulation will be run.

__init__(model, pKa, temperature)[source]

Construct a ReferenceEnergyFinder.

Parameters:

  • model (ConstantPH) – The model for which to determine reference energies. It must contain a single titratable residue with exactly two states. It does not matter what pH or reference energies were specified when it was created, because they will both be overwritten.

  • pKa (float) – The experimental pKa of the titratable residue. Reference energies will be chosen to match it.

  • temperature (openmm.unit.Quantity) – The temperature at which the simulation will be run.

findReferenceEnergies(iterations=20000, substeps=20)[source]

Compute the reference energies for the states of the model compound. On exit, they will be stored in the ConstantPH object.

Parameters:

  • iterations (int) – The number of Monte Carlo moves to attempt. The larger the number, the more tightly converged the results will be.

  • subsets (int) – The number of dynamics steps to integrate between Monte Carlo moves.