grand.potential module

Description

Set of functions to calibrate the excess chemical potential and standard state volume of water

Marley Samways

grand.potential.calc_mu_ex(system, topology, positions, box_vectors, temperature, n_lambdas, n_samples, n_equil, log_file)

Calculate the excess chemical potential of a water molecule in a given system, as the hydration free energy, using MBAR

Parameters

  • system (simtk.openmm.System) – System of interest

  • topology (simtk.openmm.app.Topology) – Topology of the system

  • positions (simtk.unit.Quantity) – Initial positions for the simulation

  • box_vectors (simtk.unit.Quantity) – Periodic box vectors for the system

  • temperature (simtk.unit.Quantity) – Temperature of the simulation

  • n_lambdas (int) – Number of lambda values

  • n_samples (int) – Number of energy samples to collect at each lambda value

  • n_equil (int) – Number of MD steps to run between each sample

  • log_file (str) – Name of the log file to write out

Returns

dG – Calculated free energy value

Return type

simtk.unit.Quantity

grand.potential.calc_std_volume(system, topology, positions, box_vectors, temperature, n_samples, n_equil)

Calculate the standard volume of a given system and parameters, this is the effective volume of a single molecule

Parameters

  • system (simtk.openmm.System) – System of interest

  • topology (simtk.openmm.app.Topology) – Topology of the system

  • positions (simtk.unit.Quantity) – Initial positions for the simulation

  • box_vectors (simtk.unit.Quantity) – Periodic box vectors for the system

  • temperature (simtk.unit.Quantity) – Temperature of the simulation

  • n_samples (int) – Number of volume samples to collect

  • n_equil (int) – Number of MD steps to run between each sample

Returns

std_volume – Calculated free energy value

Return type

simtk.unit.Quantity

grand.potential.get_lambda_values(lambda_in)

Calculate the lambda_sterics and lambda_electrostatics values for a given lambda. Electrostatics are decoupled from lambda=1 to 0.5, and sterics are decoupled from lambda=0.5 to 0.

Parameters

lambda_in (float) – Input lambda value

Returns

  • lambda_vdw (float) – Lambda value for steric interactions

  • lambda_ele (float) – Lambda value for electrostatic interactions