BioSimSpace.FreeEnergy.Binding¶

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

A class for configuring and running binding free energy simulations.

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

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.
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

`__init__`(system[, protocol, work_dir, …])	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.