BioSimSpace.FreeEnergy.Solvation¶
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class
BioSimSpace.FreeEnergy.Solvation(system, protocol=None, vacuum_leg=True, work_dir=None, engine=None, setup_only=False, ignore_warnings=False, show_errors=True)¶ 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, setup_only=False, ignore_warnings=False, show_errors=True)¶ Constructor.
- Parameters
system (
System) – The molecular system.protocol (
Protocol.FreeEnergy, [Protocol.FreeEnergy,) –Protocol.FreeEnergy] The simulation protocol. If one obect is passed, then the same protocol will be used for both legs of the simulation. Passing two objects enables a different protocol for each leg, e.g. a different lambda schedule, or run time.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.
setup_only (bool) – Whether to only support simulation setup. If True, then no simulation processes objects will be created, only the directory hierarchy and input files to run a simulation externally. This can be useful when you don’t intend to use BioSimSpace to run the simulation. Note that a ‘work_dir’ must also be specified.
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, vacuum_leg, …])Constructor.
analyse()Analyse the solvation free energy data.
getData([name, file_link, work_dir])Return a link to a zip file containing the data files required for post-simulation analysis.
run([serial])Run the simulation.
wait()Wait for the simulation to finish.
workDir()Return the working directory.
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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.overlap_free ([ [ float, float, … ] ]) – The overlap matrix. This gives the overlap between each window of the free leg. This parameter is only computed for the SOMD engine and will be None when GROMACS is used.
overlap_vacuum ([ [ float, float, … ] ]) – The overlap matrix. This gives the overlap between each window of the vacuum leg. This parameter is only computed for the SOMD engine and will be None when GROMACS is used.
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classmethod
getData(name='data', file_link=False, work_dir=None)¶ Return a link to a zip file containing the data files required for post-simulation analysis.
- Parameters
name (str) – The name of the zip file.
file_link (bool) – Whether to return a FileLink when working in Jupyter.
work_dir (str) – The working directory for the simulation.
- Returns
ouput – A path, or file link, to an archive of the process input.
- Return type
str, IPython.display.FileLink
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run(serial=True)¶ Run the simulation.
- Parameters
serial (bool) – Whether to run the individual processes for the lambda windows in serial.
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wait()¶ Wait for the simulation to finish.
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workDir()¶ Return the working directory.
- Returns
work_dir – The path of the working directory.
- Return type
str
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