aiida_gromacs.workflows package

Submodules

aiida_gromacs.workflows.simsetup module

aiida_gromacs

A workflow for setting up basic molecular dynamics simulations.

class aiida_gromacs.workflows.simsetup.SetupWorkChain(*args: Any, **kwargs: Any)

Bases: WorkChain

WorkChain for setting up a gromacs simulation automatically.

__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]]', '_awaitables': 'list[Awaitable]', '_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]', '_stepper': 'Stepper | None', '_uuid': 'Optional[uuid.UUID]'}

__module__ = 'aiida_gromacs.workflows.simsetup'

_abc_impl = <_abc._abc_data object>

classmethod define(spec)

Specify workflow recipe.

editconf()

Add simulation box to GRO file.

genion()

Add ions to system to balance charge.

gromppions()

Create a tpr for adding ions.

gromppmin()

Create a tpr for minimisation.

gromppnpt()

Create a tpr for NPT equilibration.

gromppnvt()

Create a tpr for NVT equilibration.

gromppprod()

Create a tpr for production run.

minimise()

Minimise system.

nptequilibrate()

NPT Equilibration of system system.

nvtequilibrate()

NVT Equilibration of system.

pdb2gmx()

Convert PDB file to forcefield compliant GRO file

prodmd()

Run production MD

result()

Results

solvate()

Add solvent to GRO file.

Module contents

aiida_gromacs

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