BioSimSpace.FreeEnergy.Binding¶
-
class
BioSimSpace.FreeEnergy.
Binding
(system, protocol=None, box=None, angles=[90.0000 degrees, 90.0000 degrees, 90.0000 degrees], free_leg=True, work_dir=None, engine=None, property_map={}, ignore_warnings=False, show_errors=True)¶ A class for configuring and running binding free energy simulations.
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__init__
(system, protocol=None, box=None, angles=[90.0000 degrees, 90.0000 degrees, 90.0000 degrees], free_leg=True, work_dir=None, engine=None, property_map={}, ignore_warnings=False, show_errors=True)¶ Constructor.
- Parameters
system (
System
) – The molecular system.protocol (
Protocol.FreeEnergy
) – The simulation protocol.box ([
Length
]) – A list containing the box size in each dimension: x, y, and z. 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.angles ([
Length
]) – A list containing the angles between the box vectors: yz, xz, and xy.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” }
ignore_warnings (bool) – Whether to ignore warnings when generating the binary run file. This option is specific to GROMACS and will be ignored when a different molecular dynamics engine is chosen.
show_errors (bool) – Whether to show warning/error messages when generating the binary run file. This option is specific to GROMACS and will be ignored when a different molecular dynamics engine is chosen.
Methods
__init__
(system[, protocol, box, angles, …])Constructor.
analyse
()Analyse the binding free energy data.
run
()Run the simulation.
-
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.
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run
()¶ Run the simulation.
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