BioSimSpace.FreeEnergy.analyse

BioSimSpace.FreeEnergy.analyse(work_dir, simulation_type=None)

Analyse existing free-energy data from a simulation working directory.

For the return values, leg0 refers to the simulation leg with the larger number of molecules, i.e. the “bound” leg for a “binding” free-energy simulation, or the “free” leg for a “solvation” free-energy simulation.

Parameters

• work_dir (str) – The working directory for the simulation.

• simulation_type (str) – The type of free-energy perturbation simulation_type. Options are: “solvation”, or “binding”. This allows use of a single “work_dir” for combined “solvation” and “binding” free-energy simulations. If None, then BioSimSpace will attempt to figure out the simulation type from the directory structure within “work_dir”.

Returns

• pmf0 ([(float, Energy, Energy)]) – The potential of mean force (PMF) for the first leg of the simulation. The data is a list of tuples, where each tuple contains the lambda value, the PMF, and the standard error.

• pmf1 ([(float, Energy, Energy)]) – The potential of mean force (PMF) for the second 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 free energy difference and its associated error.

• overlap0 ([ [ float, float, … ] ]) – The overlap matrix. This gives the overlap between each window of the first leg. This parameter is only computed for the SOMD engine and will be None when GROMACS is used.

• overlap1 ([ [ float, float, … ] ]) – The overlap matrix. This gives the overlap between each window of the second leg. This parameter is only computed for the SOMD engine and will be None when GROMACS is used.