BioSimSpace.FreeEnergy.Solvation¶
-
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.
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__init__
(system, protocol=None, vacuum_leg=True, work_dir=None, engine=None)¶ Constructor.
- Parameters
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.
Methods
__init__
(system[, protocol, vacuum_leg, …])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.
-
run
()¶ Run the simulation.
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