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

Author(s): James Gebbie-Rayet

Contact: james.gebbie@stfc.ac.uk

How to use from python: import aiida_gromacs

Most recent version:

Compatibility:

Plugins provided by the package

Calculations 7 Parsers 7 Data 6 Workflows 1

CalcJobs and calculation functions (aiida.calculations)

• general-MD
  class aiida_gromacs.calculations.generalMD:GeneralCalculation
• 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

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)

• general-MD
  class aiida_gromacs.parsers.generalMD:GeneralParser
• 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