# BioSimSpace.FreeEnergy.Binding¶

class BioSimSpace.FreeEnergy.Binding(system, protocol=None, box=None, work_dir=None, engine=None, property_map={})

A class for configuring and running binding free energy simulations.

__init__(system, protocol=None, box=None, work_dir=None, engine=None, property_map={})

Constructor.

Parameters
• system (System) – The molecular system.

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

• box ([Length]) – A list containing the box size in each dimension. 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.

• 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” }

Methods

 __delattr__ Implement delattr(self, name). __dir__ Default dir() implementation. __eq__ Return self==value. __format__ Default object formatter. __ge__ Return self>=value. __getattribute__ Return getattr(self, name). __gt__ Return self>value. __hash__ Return hash(self). __init__(system[, protocol, box, work_dir, …]) Constructor. __init_subclass__ This method is called when a class is subclassed. __le__ Return self<=value. __lt__ Return self

Attributes

 __dict__ __doc__ __module__ __weakref__ list of weak references to the object (if defined) _analyse_freenrg _engines
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.