BioSimSpace.FreeEnergy.Solvation

class BioSimSpace.FreeEnergy.Solvation(system, protocol=None, work_dir=None, engine=None)

A class for configuring and running solvation free energy simulations.

__init__(system, protocol=None, work_dir=None, engine=None)

Constructor.

Parameters:
  • system (System) – The molecular system.
  • protocol (Protocol.FreeEnergy) – The simulation protocol.
  • work_dir (str) – The working directory for the simulation.
  • engine (str) – The molecular dynamics engine used to run the simulation. Available options are “GROMACS”, or “SOMD”. If this argument is omitted then BioSimSpace will choose an appropriate engine for you.

Methods

__init__(system[, protocol, work_dir, engine]) Constructor.
analyse() Analyse the solvation free energy data.
run() Run the simulation.
analyse()

Analyse the solvation free energy data.

Returns:
  • pmf_free ([(float, Energy, Energy)]) – The potential of mean force (PMF) for the free leg of the simulation. The data is a list of tuples, where each tuple contains the lambda value, the PMF, and the standard error.
  • pmf_vacuum ([(float, Energy, Energy)]) – The potential of mean force (PMF) for the vacuum leg of the simulation. The data is a list of tuples, where each tuple contains the lambda value, the PMF, and the standard error.
  • free_energy ((Energy, Energy)) – The solvation free energy difference and its associated error.
run()

Run the simulation.