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({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.editconf'

_abc_impl = <_abc._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({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.genericMD'

_abc_impl = <_abc._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({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.genion'

_abc_impl = <_abc._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({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.grompp'

_abc_impl = <_abc._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.make_ndx module

Calculations provided by aiida_gromacs.

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

class aiida_gromacs.calculations.make_ndx.Make_ndxCalculation(*args: Any, **kwargs: Any)

Bases: CalcJob

AiiDA calculation plugin wrapping the ‘gmx make_ndx’ executable.

AiiDA plugin wrapper for converting PDB files to GRO files.

__abstractmethods__ = frozenset({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.make_ndx'

_abc_impl = <_abc._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({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.mdrun'

_abc_impl = <_abc._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({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.pdb2gmx'

_abc_impl = <_abc._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({})

__annotations__ = {'CLASS_NAME': 'str', 'SINGLE_OUTPUT_LINKNAME': 'str', 'STATES': 'Optional[Sequence[Type[State]]]', '_STATES_MAP': 'Optional[Dict[Hashable, Type[State]]]', '__called': 'bool', '_auto_persist': 'Optional[Set[str]]', '_cleanups': 'Optional[List[Callable[[], None]]]', '_creation_time': 'Optional[float]', '_event_callbacks': 'Dict[Hashable, List[EVENT_CALLBACK_TYPE]]', '_interrupt_action': 'Optional[futures.CancellableAction]', '_killing': 'Optional[futures.CancellableAction]', '_node': 'Optional[orm.ProcessNode]', '_outputs': 'Dict[str, Any]', '_parsed_inputs': 'Optional[utils.AttributesFrozendict]', '_paused': 'Optional[persistence.SavableFuture]', '_pausing': 'Optional[futures.CancellableAction]', '_pre_paused_status': 'Optional[str]', '_state': 'Optional[State]', '_status': 'Optional[str]', '_uuid': 'Optional[uuid.UUID]', 'link_label_retrieved': 'str'}

__module__ = 'aiida_gromacs.calculations.solvate'

_abc_impl = <_abc._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.