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

A class for configuring and running solvation free energy simulations.

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


  • 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.


__delattr__(name, /)

Implement delattr(self, name).


Default dir() implementation.

__eq__(value, /)

Return self==value.

__format__(format_spec, /)

Default object formatter.

__ge__(value, /)

Return self>=value.

__getattribute__(name, /)

Return getattr(self, name).

__gt__(value, /)

Return self>value.


Return hash(self).

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



This method is called when a class is subclassed.

__le__(value, /)

Return self<=value.

__lt__(value, /)

Return self<value.

__ne__(value, /)

Return self!=value.


Create and return a new object.


Helper for pickle.

__reduce_ex__(protocol, /)

Helper for pickle.


Return repr(self).

__setattr__(name, value, /)

Implement setattr(self, name, value).


Size of object in memory, in bytes.


Return str(self).


Abstract classes can override this to customize issubclass().


Analyse the GROMACS free energy data.


Analyse the SOMD free energy data.

_initialise_runner(system0, system1)

Internal helper function to initialise the process runner.


Internal function to update run arguments for all subprocesses.


Analyse the solvation free energy data.


Run the simulation.






list of weak references to the object (if defined)