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AiiDA plugin package "aiida-gromacs"

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General information

Current state:

Short description: A plugin for using GROMACS with AiiDA for molecular dymanics simulations.

How to install: pip install git+https://github.com/jimboid/aiida-gromacs

Source code: Go to the source code repository

Documentation: Go to plugin documentation

Detailed information

Author(s): James Gebbie-Rayet

Contact: james.gebbie@stfc.ac.uk

How to use from python: import aiida_gromacs

Most recent version: 0.1.0

Compatibility:

Plugins provided by the package

Calculations 6 Parsers 6 Data 6 Workflows 1 Other (Data commands) 1

CalcJobs and calculation functions (aiida.calculations)

  • gromacs.editconf
    class aiida_gromacs.calculations.editconf:EditconfCalculation
  • gromacs.genion
    class aiida_gromacs.calculations.genion:GenionCalculation
  • gromacs.grompp
    class aiida_gromacs.calculations.grompp:GromppCalculation
  • gromacs.mdrun
    class aiida_gromacs.calculations.mdrun:MdrunCalculation
  • gromacs.pdb2gmx
    class aiida_gromacs.calculations.pdb2gmx:Pdb2gmxCalculation
  • gromacs.solvate
    class aiida_gromacs.calculations.solvate:SolvateCalculation

verdi data commands (aiida.cmdline.data)

  • gromacs
    class aiida_gromacs.cli:data_cli

Data node types (aiida.data)

  • gromacs.editconf
    class aiida_gromacs.data.editconf:EditconfParameters
  • gromacs.genion
    class aiida_gromacs.data.genion:GenionParameters
  • gromacs.grompp
    class aiida_gromacs.data.grompp:GromppParameters
  • gromacs.mdrun
    class aiida_gromacs.data.mdrun:MdrunParameters
  • gromacs.pdb2gmx
    class aiida_gromacs.data.pdb2gmx:Pdb2gmxParameters
  • gromacs.solvate
    class aiida_gromacs.data.solvate:SolvateParameters

CalcJob parsers (aiida.parsers)

  • gromacs.editconf
    class aiida_gromacs.parsers.editconf:EditconfParser
  • gromacs.genion
    class aiida_gromacs.parsers.genion:GenionParser
  • gromacs.grompp
    class aiida_gromacs.parsers.grompp:GromppParser
  • gromacs.mdrun
    class aiida_gromacs.parsers.mdrun:MdrunParser
  • gromacs.pdb2gmx
    class aiida_gromacs.parsers.pdb2gmx:Pdb2gmxParser
  • gromacs.solvate
    class aiida_gromacs.parsers.solvate:SolvateParser

WorkChains and work functions (aiida.workflows)

  • gromacs.setup
    class aiida_gromacs.workflows.simsetup:SetupWorkChain