aiida_gromacs package

Subpackages

• aiida_gromacs.calculations package
  • Submodules
  • aiida_gromacs.calculations.editconf module
    • EditconfCalculation
      • EditconfCalculation.__abstractmethods__
      • EditconfCalculation.__annotations__
      • EditconfCalculation.__module__
      • EditconfCalculation._abc_impl
      • EditconfCalculation.define()
      • EditconfCalculation.prepare_for_submission()
  • aiida_gromacs.calculations.genericMD module
    • GenericCalculation
      • GenericCalculation.__abstractmethods__
      • GenericCalculation.__annotations__
      • GenericCalculation.__module__
      • GenericCalculation._abc_impl
      • GenericCalculation.define()
      • GenericCalculation.prepare_for_submission()
  • aiida_gromacs.calculations.genion module
    • GenionCalculation
      • GenionCalculation.__abstractmethods__
      • GenionCalculation.__annotations__
      • GenionCalculation.__module__
      • GenionCalculation._abc_impl
      • GenionCalculation.define()
      • GenionCalculation.prepare_for_submission()
  • aiida_gromacs.calculations.grompp module
    • GromppCalculation
      • GromppCalculation.__abstractmethods__
      • GromppCalculation.__annotations__
      • GromppCalculation.__module__
      • GromppCalculation._abc_impl
      • GromppCalculation.define()
      • GromppCalculation.prepare_for_submission()
  • aiida_gromacs.calculations.make_ndx module
    • Make_ndxCalculation
      • Make_ndxCalculation.__abstractmethods__
      • Make_ndxCalculation.__annotations__
      • Make_ndxCalculation.__module__
      • Make_ndxCalculation._abc_impl
      • Make_ndxCalculation.define()
      • Make_ndxCalculation.prepare_for_submission()
  • aiida_gromacs.calculations.mdrun module
    • MdrunCalculation
      • MdrunCalculation.__abstractmethods__
      • MdrunCalculation.__annotations__
      • MdrunCalculation.__module__
      • MdrunCalculation._abc_impl
      • MdrunCalculation.define()
      • MdrunCalculation.prepare_for_submission()
  • aiida_gromacs.calculations.pdb2gmx module
    • Pdb2gmxCalculation
      • Pdb2gmxCalculation.__abstractmethods__
      • Pdb2gmxCalculation.__annotations__
      • Pdb2gmxCalculation.__module__
      • Pdb2gmxCalculation._abc_impl
      • Pdb2gmxCalculation.define()
      • Pdb2gmxCalculation.prepare_for_submission()
  • aiida_gromacs.calculations.solvate module
    • SolvateCalculation
      • SolvateCalculation.__abstractmethods__
      • SolvateCalculation.__annotations__
      • SolvateCalculation.__module__
      • SolvateCalculation._abc_impl
      • SolvateCalculation.define()
      • SolvateCalculation.prepare_for_submission()
  • 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._plugin_type_string
      • EditconfParameters._query_type_string
      • 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._plugin_type_string
      • GenionParameters._query_type_string
      • 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._plugin_type_string
      • GromppParameters._query_type_string
      • 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._plugin_type_string
      • Make_ndxParameters._query_type_string
      • 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._plugin_type_string
      • MdrunParameters._query_type_string
      • 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._plugin_type_string
      • Pdb2gmxParameters._query_type_string
      • 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._plugin_type_string
      • SolvateParameters._query_type_string
      • SolvateParameters.cmdline_params()
      • SolvateParameters.schema
      • SolvateParameters.validate()
  • Module contents
• aiida_gromacs.parsers package
  • Submodules
  • aiida_gromacs.parsers.editconf module
    • EditconfParser
      • EditconfParser.__abstractmethods__
      • EditconfParser.__annotations__
      • EditconfParser.__init__()
      • EditconfParser.__module__
      • EditconfParser._abc_impl
      • EditconfParser.parse()
  • aiida_gromacs.parsers.genericMD module
    • GenericParser
      • GenericParser.__abstractmethods__
      • GenericParser.__annotations__
      • GenericParser.__init__()
      • GenericParser.__module__
      • GenericParser._abc_impl
      • GenericParser._parse_gromacs_top()
      • GenericParser.format_link_label()
      • GenericParser.parse()
  • aiida_gromacs.parsers.genion module
    • GenionParser
      • GenionParser.__abstractmethods__
      • GenionParser.__annotations__
      • GenionParser.__init__()
      • GenionParser.__module__
      • GenionParser._abc_impl
      • GenionParser.parse()
  • aiida_gromacs.parsers.grompp module
    • GromppParser
      • GromppParser.__abstractmethods__
      • GromppParser.__annotations__
      • GromppParser.__init__()
      • GromppParser.__module__
      • GromppParser._abc_impl
      • GromppParser.parse()
  • aiida_gromacs.parsers.make_ndx module
    • Make_ndxParser
      • Make_ndxParser.__abstractmethods__
      • Make_ndxParser.__annotations__
      • Make_ndxParser.__init__()
      • Make_ndxParser.__module__
      • Make_ndxParser._abc_impl
      • Make_ndxParser.parse()
  • aiida_gromacs.parsers.mdrun module
    • MdrunParser
      • MdrunParser.__abstractmethods__
      • MdrunParser.__annotations__
      • MdrunParser.__init__()
      • MdrunParser.__module__
      • MdrunParser._abc_impl
      • MdrunParser.output_parsed_metadata()
      • MdrunParser.parse()
      • MdrunParser.parse_file_contents()
  • aiida_gromacs.parsers.pdb2gmx module
    • Pdb2gmxParser
      • Pdb2gmxParser.__abstractmethods__
      • Pdb2gmxParser.__annotations__
      • Pdb2gmxParser.__init__()
      • Pdb2gmxParser.__module__
      • Pdb2gmxParser._abc_impl
      • Pdb2gmxParser.parse()
  • aiida_gromacs.parsers.solvate module
    • SolvateParser
      • SolvateParser.__abstractmethods__
      • SolvateParser.__annotations__
      • SolvateParser.__init__()
      • SolvateParser.__module__
      • SolvateParser._abc_impl
      • SolvateParser.parse()
  • 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

1. An AiiDA localhost computer

2. 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)

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.orm.nodes.data.code.portable.PortableCode

aiida_gromacs.helpers.get_computer(name='localhost', workdir=None)

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.orm.computers.Computer

aiida_gromacs.helpers.get_path_to_executable(executable)

Get path to local executable.

Parameters:

executable (str) – Name of executable in the $PATH variable

Returns:

path to executable

Return type:

str

Module contents

aiida_gromacs

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