aiida_gromacs package¶
Subpackages¶
- aiida_gromacs.calculations package
- Submodules
- aiida_gromacs.calculations.editconf module
- aiida_gromacs.calculations.genericMD module
- aiida_gromacs.calculations.genion module
- aiida_gromacs.calculations.grompp module
- aiida_gromacs.calculations.make_ndx module
- aiida_gromacs.calculations.mdrun module
- aiida_gromacs.calculations.pdb2gmx module
- aiida_gromacs.calculations.solvate module
- Module contents
- aiida_gromacs.data package
- Submodules
- aiida_gromacs.data.editconf module
EditconfParameters
EditconfParameters.__abstractmethods__
EditconfParameters.__annotations__
EditconfParameters.__init__()
EditconfParameters.__module__
EditconfParameters.__parameters__
EditconfParameters.__str__()
EditconfParameters._abc_impl
EditconfParameters._logger
EditconfParameters.cmdline_params()
EditconfParameters.schema
EditconfParameters.validate()
- aiida_gromacs.data.genion module
GenionParameters
GenionParameters.__abstractmethods__
GenionParameters.__annotations__
GenionParameters.__init__()
GenionParameters.__module__
GenionParameters.__parameters__
GenionParameters.__str__()
GenionParameters._abc_impl
GenionParameters._logger
GenionParameters.cmdline_params()
GenionParameters.schema
GenionParameters.validate()
- aiida_gromacs.data.grompp module
GromppParameters
GromppParameters.__abstractmethods__
GromppParameters.__annotations__
GromppParameters.__init__()
GromppParameters.__module__
GromppParameters.__parameters__
GromppParameters.__str__()
GromppParameters._abc_impl
GromppParameters._logger
GromppParameters.cmdline_params()
GromppParameters.schema
GromppParameters.validate()
- aiida_gromacs.data.make_ndx module
Make_ndxParameters
Make_ndxParameters.__abstractmethods__
Make_ndxParameters.__annotations__
Make_ndxParameters.__init__()
Make_ndxParameters.__module__
Make_ndxParameters.__parameters__
Make_ndxParameters.__str__()
Make_ndxParameters._abc_impl
Make_ndxParameters._logger
Make_ndxParameters.cmdline_params()
Make_ndxParameters.schema
Make_ndxParameters.validate()
- aiida_gromacs.data.mdrun module
MdrunParameters
MdrunParameters.__abstractmethods__
MdrunParameters.__annotations__
MdrunParameters.__init__()
MdrunParameters.__module__
MdrunParameters.__parameters__
MdrunParameters.__str__()
MdrunParameters._abc_impl
MdrunParameters._logger
MdrunParameters.cmdline_params()
MdrunParameters.schema
MdrunParameters.validate()
- aiida_gromacs.data.pdb2gmx module
Pdb2gmxParameters
Pdb2gmxParameters.__abstractmethods__
Pdb2gmxParameters.__annotations__
Pdb2gmxParameters.__init__()
Pdb2gmxParameters.__module__
Pdb2gmxParameters.__parameters__
Pdb2gmxParameters.__str__()
Pdb2gmxParameters._abc_impl
Pdb2gmxParameters._logger
Pdb2gmxParameters.cmdline_params()
Pdb2gmxParameters.schema
Pdb2gmxParameters.validate()
- aiida_gromacs.data.solvate module
SolvateParameters
SolvateParameters.__abstractmethods__
SolvateParameters.__annotations__
SolvateParameters.__init__()
SolvateParameters.__module__
SolvateParameters.__parameters__
SolvateParameters.__str__()
SolvateParameters._abc_impl
SolvateParameters._logger
SolvateParameters.cmdline_params()
SolvateParameters.schema
SolvateParameters.validate()
- Module contents
- aiida_gromacs.parsers package
- Submodules
- aiida_gromacs.parsers.editconf module
- aiida_gromacs.parsers.genericMD module
- aiida_gromacs.parsers.genion module
- aiida_gromacs.parsers.grompp module
- aiida_gromacs.parsers.make_ndx module
- aiida_gromacs.parsers.mdrun module
- aiida_gromacs.parsers.pdb2gmx module
- aiida_gromacs.parsers.solvate module
- Module contents
- aiida_gromacs.workflows package
- Submodules
- aiida_gromacs.workflows.simsetup module
SetupWorkChain
SetupWorkChain.__abstractmethods__
SetupWorkChain.__annotations__
SetupWorkChain.__module__
SetupWorkChain._abc_impl
SetupWorkChain.define()
SetupWorkChain.editconf()
SetupWorkChain.genion()
SetupWorkChain.gromppions()
SetupWorkChain.gromppmin()
SetupWorkChain.gromppnpt()
SetupWorkChain.gromppnvt()
SetupWorkChain.gromppprod()
SetupWorkChain.minimise()
SetupWorkChain.nptequilibrate()
SetupWorkChain.nvtequilibrate()
SetupWorkChain.pdb2gmx()
SetupWorkChain.prodmd()
SetupWorkChain.result()
SetupWorkChain.solvate()
- Module contents
Submodules¶
aiida_gromacs.helpers module¶
Helper functions for automatically setting up computer & code. Helper functions for setting up
An AiiDA localhost computer
A “gmx” code on localhost
Note: Point 2 is made possible by the fact that the diff
executable is
available in the PATH on almost any UNIX system.
- aiida_gromacs.helpers.get_code(entry_point, computer)[source]¶
Get local code. Sets up code for given entry point on given computer.
- Parameters:
entry_point – Entry point of calculation plugin
computer – (local) AiiDA computer
- Returns:
The code node
- Return type:
- aiida_gromacs.helpers.get_computer(name='localhost', workdir=None)[source]¶
Get AiiDA computer. Loads computer ‘name’ from the database, if exists. Sets up local computer ‘name’, if it isn’t found in the DB.
- Parameters:
name – Name of computer to load or set up.
workdir – path to work directory Used only when creating a new computer.
- Returns:
The computer node
- Return type:
- aiida_gromacs.helpers.setup_generic_code(code)[source]¶
Try to set up any code for running a genericMD process
- Parameters:
code – executable@computer of the code being run
Module contents¶
aiida_gromacs
A plugin for using GROMACS with AiiDA for molecular dymanics simulations.