BioSimSpace.FreeEnergy.Solvation

class BioSimSpace.FreeEnergy.Solvation(system, protocol=None, vacuum_leg=True, work_dir=None, engine=None, ignore_warnings=False, show_errors=True)

A class for configuring and running solvation free energy simulations.

__init__(system, protocol=None, vacuum_leg=True, work_dir=None, engine=None, ignore_warnings=False, show_errors=True)

Constructor.

Parameters
  • system (System) – The molecular system.

  • protocol (Protocol.FreeEnergy) – The simulation protocol.

  • vacuum_leg (bool) – Whether to simulation the vacuum leg of the simulation. Set to False if you only wish to run the free leg.

  • 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.

  • ignore_warnings (bool) – Whether to ignore warnings when generating the binary run file. This option is specific to GROMACS and will be ignored when a different molecular dynamics engine is chosen.

  • show_errors (bool) – Whether to show warning/error messages when generating the binary run file. This option is specific to GROMACS and will be ignored when a different molecular dynamics engine is chosen.

Methods

__init__(system[, protocol, vacuum_leg, …])

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.