aiida_gromacs.calculations package

Submodules

aiida_gromacs.calculations.editconf module

Calculations provided by aiida_gromacs.

This calculation configures the ability to use the ‘gmx editconf’ executable.

class aiida_gromacs.calculations.editconf.EditconfCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the ‘gmx editconf’ executable.

AiiDA plugin wrapper for adding a simulation box to structure file.

__abstractmethods__ = frozenset({})

__module__ = 'aiida_gromacs.calculations.editconf'

_abc_impl = <_abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_gromacs.calculations.genericMD module

Generic calculation used to track input and output files of a generic command.

class aiida_gromacs.calculations.genericMD.GenericCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping an executable with user defined input and output files.

__abstractmethods__ = frozenset({})

__module__ = 'aiida_gromacs.calculations.genericMD'

_abc_impl = <_abc_data object>

classmethod define(spec)

AiiDA plugin wrapper for running an arbitrary command.

prepare_for_submission(folder)

Create input files in the format the code external to AiiDA expects and return CalcInfo object that contains instructions for AiiDA engine on how the code should be run.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_gromacs.calculations.genion module

Calculations provided by aiida_gromacs.

This calculation configures the ability to use the ‘gmx genion’ executable.

class aiida_gromacs.calculations.genion.GenionCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the ‘gmx genion’ executable.

AiiDA plugin wrapper for converting PDB files to GRO files.

__abstractmethods__ = frozenset({})

__module__ = 'aiida_gromacs.calculations.genion'

_abc_impl = <_abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_gromacs.calculations.grompp module

Calculations provided by aiida_gromacs.

This calculation configures the ability to use the ‘gmx grompp’ executable.

class aiida_gromacs.calculations.grompp.GromppCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the ‘gmx grompp’ executable.

AiiDA plugin wrapper for converting PDB files to GRO files.

__abstractmethods__ = frozenset({})

__module__ = 'aiida_gromacs.calculations.grompp'

_abc_impl = <_abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_gromacs.calculations.mdrun module

Calculations provided by aiida_gromacs.

This calculation configures the ability to use the ‘gmx mdrun’ executable.

class aiida_gromacs.calculations.mdrun.MdrunCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the ‘gmx mdrun’ executable.

AiiDA plugin wrapper for converting PDB files to GRO files.

__abstractmethods__ = frozenset({})

__module__ = 'aiida_gromacs.calculations.mdrun'

_abc_impl = <_abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_gromacs.calculations.pdb2gmx module

Calculations provided by aiida_gromacs.

This calculation configures the ability to use the ‘gmx pdb2gmx’ executable.

class aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the ‘gmx pdb2gmx’ executable.

AiiDA plugin wrapper for converting PDB files to GRO files.

__abstractmethods__ = frozenset({})

__module__ = 'aiida_gromacs.calculations.pdb2gmx'

_abc_impl = <_abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

aiida_gromacs.calculations.solvate module

Calculations provided by aiida_gromacs.

This calculation configures the ability to use the ‘gmx solvate’ executable.

class aiida_gromacs.calculations.solvate.SolvateCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the ‘gmx solvate’ executable.

AiiDA plugin wrapper for solvating a molecular system.

__abstractmethods__ = frozenset({})

__module__ = 'aiida_gromacs.calculations.solvate'

_abc_impl = <_abc_data object>

classmethod define(spec)

Define inputs and outputs of the calculation.

prepare_for_submission(folder)

Create input files.

Parameters:

folder – an aiida.common.folders.Folder where the plugin should temporarily place all files needed by the calculation.

Returns:

aiida.common.datastructures.CalcInfo instance

Module contents

aiida_gromacs

A plugin for using GROMACS with AiiDA for molecular dymanics simulations.