BioSimSpace.FreeEnergy.Binding

class BioSimSpace.FreeEnergy.Binding(system, protocol=None, box=None, angles=[90.0000 degrees, 90.0000 degrees, 90.0000 degrees], free_leg=True, work_dir=None, engine=None, property_map={}, ignore_warnings=False, show_errors=True)

A class for configuring and running binding free energy simulations.

__init__(system, protocol=None, box=None, angles=[90.0000 degrees, 90.0000 degrees, 90.0000 degrees], free_leg=True, work_dir=None, engine=None, property_map={}, ignore_warnings=False, show_errors=True)

Constructor.

Parameters

  • system (System) – The molecular system.

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

  • box ([Length]) – A list containing the box size in each dimension: x, y, and z. This box will be used for the “free” leg of the simulation, which typically can be run with a significantly smaller box than the “bound” leg.

  • angles ([Length]) – A list containing the angles between the box vectors: yz, xz, and xy.

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

  • property_map (dict) – A dictionary that maps system “properties” to their user defined values. This allows the user to refer to properties with their own naming scheme, e.g. { “charge” : “my-charge” }

  • 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, box, angles, …])

Constructor.

analyse()

Analyse the binding free energy data.

run()

Run the simulation.
analyse()

Analyse the binding 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 binding free energy difference and its associated error.

run()

Run the simulation.