BioSimSpace.FreeEnergy.Binding

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

A class for configuring and running binding free energy simulations.

__init__(system, protocol=None, box=None, free_leg=True, 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.

• 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” }

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, free_leg, …])	Constructor.
__init_subclass__	This method is called when a class is subclassed.
__le__	Return self<=value.
__lt__	Return self<value.
__ne__	Return self!=value.
__new__	Create and return a new object.
__reduce__	Helper for pickle.
__reduce_ex__	Helper for pickle.
__repr__	Return repr(self).
__setattr__	Implement setattr(self, name, value).
__sizeof__	Size of object in memory, in bytes.
__str__	Return str(self).
__subclasshook__	Abstract classes can override this to customize issubclass().
_analyse_gromacs()	Analyse the GROMACS free energy data.
_analyse_somd()	Analyse the SOMD free energy data.
_initialise_runner(system0, system1)	Internal helper function to initialise the process runner.
_update_run_args(args)	Internal function to update run arguments for all subprocesses.
analyse()	Analyse the binding free energy data.
run()	Run the simulation.

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.