Index

_

__abstractmethods__ (aiida_gromacs.calculations.editconf.EditconfCalculation attribute) (aiida_gromacs.calculations.genericMD.GenericCalculation attribute) (aiida_gromacs.calculations.genion.GenionCalculation attribute) (aiida_gromacs.calculations.grompp.GromppCalculation attribute) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation attribute) (aiida_gromacs.calculations.mdrun.MdrunCalculation attribute) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation attribute) (aiida_gromacs.calculations.solvate.SolvateCalculation attribute) (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute) (aiida_gromacs.parsers.editconf.EditconfParser attribute) (aiida_gromacs.parsers.genericMD.GenericParser attribute) (aiida_gromacs.parsers.genion.GenionParser attribute) (aiida_gromacs.parsers.grompp.GromppParser attribute) (aiida_gromacs.parsers.make_ndx.Make_ndxParser attribute) (aiida_gromacs.parsers.mdrun.MdrunParser attribute) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser attribute) (aiida_gromacs.parsers.solvate.SolvateParser attribute) (aiida_gromacs.workflows.simsetup.SetupWorkChain attribute) __annotations__ (aiida_gromacs.calculations.editconf.EditconfCalculation attribute) (aiida_gromacs.calculations.genericMD.GenericCalculation attribute) (aiida_gromacs.calculations.genion.GenionCalculation attribute) (aiida_gromacs.calculations.grompp.GromppCalculation attribute) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation attribute) (aiida_gromacs.calculations.mdrun.MdrunCalculation attribute) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation attribute) (aiida_gromacs.calculations.solvate.SolvateCalculation attribute) (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute) (aiida_gromacs.parsers.editconf.EditconfParser attribute) (aiida_gromacs.parsers.genericMD.GenericParser attribute) (aiida_gromacs.parsers.genion.GenionParser attribute) (aiida_gromacs.parsers.grompp.GromppParser attribute) (aiida_gromacs.parsers.make_ndx.Make_ndxParser attribute) (aiida_gromacs.parsers.mdrun.MdrunParser attribute) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser attribute) (aiida_gromacs.parsers.solvate.SolvateParser attribute) (aiida_gromacs.workflows.simsetup.SetupWorkChain attribute) __firstlineno__ (aiida_gromacs.calculations.editconf.EditconfCalculation attribute) (aiida_gromacs.calculations.genericMD.GenericCalculation attribute) (aiida_gromacs.calculations.genion.GenionCalculation attribute) (aiida_gromacs.calculations.grompp.GromppCalculation attribute) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation attribute) (aiida_gromacs.calculations.mdrun.MdrunCalculation attribute) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation attribute) (aiida_gromacs.calculations.solvate.SolvateCalculation attribute) (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute) (aiida_gromacs.parsers.editconf.EditconfParser attribute) (aiida_gromacs.parsers.genericMD.GenericParser attribute) (aiida_gromacs.parsers.genion.GenionParser attribute) (aiida_gromacs.parsers.grompp.GromppParser attribute) (aiida_gromacs.parsers.make_ndx.Make_ndxParser attribute) (aiida_gromacs.parsers.mdrun.MdrunParser attribute) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser attribute) (aiida_gromacs.parsers.solvate.SolvateParser attribute) (aiida_gromacs.workflows.simsetup.SetupWorkChain attribute) __init__() (aiida_gromacs.data.editconf.EditconfParameters method) (aiida_gromacs.data.genion.GenionParameters method) (aiida_gromacs.data.grompp.GromppParameters method) (aiida_gromacs.data.make_ndx.Make_ndxParameters method) (aiida_gromacs.data.mdrun.MdrunParameters method) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters method) (aiida_gromacs.data.solvate.SolvateParameters method) (aiida_gromacs.parsers.editconf.EditconfParser method) (aiida_gromacs.parsers.genericMD.GenericParser method) (aiida_gromacs.parsers.genion.GenionParser method) (aiida_gromacs.parsers.grompp.GromppParser method) (aiida_gromacs.parsers.make_ndx.Make_ndxParser method) (aiida_gromacs.parsers.mdrun.MdrunParser method) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser method) (aiida_gromacs.parsers.solvate.SolvateParser method) __module__ (aiida_gromacs.calculations.editconf.EditconfCalculation attribute) (aiida_gromacs.calculations.genericMD.GenericCalculation attribute) (aiida_gromacs.calculations.genion.GenionCalculation attribute) (aiida_gromacs.calculations.grompp.GromppCalculation attribute) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation attribute) (aiida_gromacs.calculations.mdrun.MdrunCalculation attribute) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation attribute) (aiida_gromacs.calculations.solvate.SolvateCalculation attribute) (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute) (aiida_gromacs.parsers.editconf.EditconfParser attribute) (aiida_gromacs.parsers.genericMD.GenericParser attribute) (aiida_gromacs.parsers.genion.GenionParser attribute) (aiida_gromacs.parsers.grompp.GromppParser attribute) (aiida_gromacs.parsers.make_ndx.Make_ndxParser attribute) (aiida_gromacs.parsers.mdrun.MdrunParser attribute) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser attribute) (aiida_gromacs.parsers.solvate.SolvateParser attribute) (aiida_gromacs.workflows.simsetup.SetupWorkChain attribute)

__parameters__ (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute) __static_attributes__ (aiida_gromacs.calculations.editconf.EditconfCalculation attribute) (aiida_gromacs.calculations.genericMD.GenericCalculation attribute) (aiida_gromacs.calculations.genion.GenionCalculation attribute) (aiida_gromacs.calculations.grompp.GromppCalculation attribute) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation attribute) (aiida_gromacs.calculations.mdrun.MdrunCalculation attribute) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation attribute) (aiida_gromacs.calculations.solvate.SolvateCalculation attribute) (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute) (aiida_gromacs.parsers.editconf.EditconfParser attribute) (aiida_gromacs.parsers.genericMD.GenericParser attribute) (aiida_gromacs.parsers.genion.GenionParser attribute) (aiida_gromacs.parsers.grompp.GromppParser attribute) (aiida_gromacs.parsers.make_ndx.Make_ndxParser attribute) (aiida_gromacs.parsers.mdrun.MdrunParser attribute) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser attribute) (aiida_gromacs.parsers.solvate.SolvateParser attribute) (aiida_gromacs.workflows.simsetup.SetupWorkChain attribute) __str__() (aiida_gromacs.data.editconf.EditconfParameters method) (aiida_gromacs.data.genion.GenionParameters method) (aiida_gromacs.data.grompp.GromppParameters method) (aiida_gromacs.data.make_ndx.Make_ndxParameters method) (aiida_gromacs.data.mdrun.MdrunParameters method) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters method) (aiida_gromacs.data.solvate.SolvateParameters method) _abc_impl (aiida_gromacs.calculations.editconf.EditconfCalculation attribute) (aiida_gromacs.calculations.genericMD.GenericCalculation attribute) (aiida_gromacs.calculations.genion.GenionCalculation attribute) (aiida_gromacs.calculations.grompp.GromppCalculation attribute) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation attribute) (aiida_gromacs.calculations.mdrun.MdrunCalculation attribute) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation attribute) (aiida_gromacs.calculations.solvate.SolvateCalculation attribute) (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute) (aiida_gromacs.parsers.editconf.EditconfParser attribute) (aiida_gromacs.parsers.genericMD.GenericParser attribute) (aiida_gromacs.parsers.genion.GenionParser attribute) (aiida_gromacs.parsers.grompp.GromppParser attribute) (aiida_gromacs.parsers.make_ndx.Make_ndxParser attribute) (aiida_gromacs.parsers.mdrun.MdrunParser attribute) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser attribute) (aiida_gromacs.parsers.solvate.SolvateParser attribute) (aiida_gromacs.workflows.simsetup.SetupWorkChain attribute) _logger (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute)

A

add_calculation_inputs() (in module aiida_gromacs.data.plumed_input) add_calculation_outputs() (in module aiida_gromacs.data.plumed_input) aiida_gromacs module aiida_gromacs.calculations module 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 aiida_gromacs.data module aiida_gromacs.data.editconf module aiida_gromacs.data.genion module aiida_gromacs.data.grompp module aiida_gromacs.data.make_ndx module

aiida_gromacs.data.mdrun module aiida_gromacs.data.pdb2gmx module aiida_gromacs.data.plumed_input module aiida_gromacs.data.solvate module aiida_gromacs.helpers module aiida_gromacs.parsers module 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 aiida_gromacs.workflows module aiida_gromacs.workflows.simsetup module

C

calculation_inputs_outputs (aiida_gromacs.data.plumed_input.PlumedInputData property) check_trajectory_format() (aiida_gromacs.parsers.mdrun.MdrunParser method) cmdline_params() (aiida_gromacs.data.editconf.EditconfParameters method) (aiida_gromacs.data.genion.GenionParameters method) (aiida_gromacs.data.grompp.GromppParameters method) (aiida_gromacs.data.make_ndx.Make_ndxParameters method) (aiida_gromacs.data.mdrun.MdrunParameters method) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters method) (aiida_gromacs.data.solvate.SolvateParameters method)

D

define() (aiida_gromacs.calculations.editconf.EditconfCalculation class method) (aiida_gromacs.calculations.genericMD.GenericCalculation class method) (aiida_gromacs.calculations.genion.GenionCalculation class method) (aiida_gromacs.calculations.grompp.GromppCalculation class method) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation class method) (aiida_gromacs.calculations.mdrun.MdrunCalculation class method) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation class method) (aiida_gromacs.calculations.solvate.SolvateCalculation class method) (aiida_gromacs.workflows.simsetup.SetupWorkChain class method)

E

editconf() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) EditconfCalculation (class in aiida_gromacs.calculations.editconf)

EditconfParameters (class in aiida_gromacs.data.editconf) EditconfParser (class in aiida_gromacs.parsers.editconf)

F

fields (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.plumed_input.PlumedInputData attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute)

find_filename_from_string() (in module aiida_gromacs.data.plumed_input) find_plumed_filenames() (in module aiida_gromacs.data.plumed_input) format_link_label() (aiida_gromacs.parsers.genericMD.GenericParser static method)

G

GenericCalculation (class in aiida_gromacs.calculations.genericMD) GenericParser (class in aiida_gromacs.parsers.genericMD) genion() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) GenionCalculation (class in aiida_gromacs.calculations.genion) GenionParameters (class in aiida_gromacs.data.genion) GenionParser (class in aiida_gromacs.parsers.genion) get_code() (in module aiida_gromacs.helpers) get_computer() (in module aiida_gromacs.helpers)

get_path_to_executable() (in module aiida_gromacs.helpers) GromppCalculation (class in aiida_gromacs.calculations.grompp) gromppions() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) gromppmin() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) gromppnpt() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) gromppnvt() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) GromppParameters (class in aiida_gromacs.data.grompp) GromppParser (class in aiida_gromacs.parsers.grompp) gromppprod() (aiida_gromacs.workflows.simsetup.SetupWorkChain method)

I

inpfile_list (aiida_gromacs.data.plumed_input.PlumedInputData property)

M

Make_ndxCalculation (class in aiida_gromacs.calculations.make_ndx) Make_ndxParameters (class in aiida_gromacs.data.make_ndx) Make_ndxParser (class in aiida_gromacs.parsers.make_ndx) MdrunCalculation (class in aiida_gromacs.calculations.mdrun) MdrunParameters (class in aiida_gromacs.data.mdrun) MdrunParser (class in aiida_gromacs.parsers.mdrun) minimise() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) module aiida_gromacs aiida_gromacs.calculations aiida_gromacs.calculations.editconf aiida_gromacs.calculations.genericMD aiida_gromacs.calculations.genion aiida_gromacs.calculations.grompp aiida_gromacs.calculations.make_ndx aiida_gromacs.calculations.mdrun aiida_gromacs.calculations.pdb2gmx aiida_gromacs.calculations.solvate aiida_gromacs.data aiida_gromacs.data.editconf aiida_gromacs.data.genion aiida_gromacs.data.grompp aiida_gromacs.data.make_ndx aiida_gromacs.data.mdrun aiida_gromacs.data.pdb2gmx aiida_gromacs.data.plumed_input aiida_gromacs.data.solvate aiida_gromacs.helpers aiida_gromacs.parsers aiida_gromacs.parsers.editconf aiida_gromacs.parsers.genericMD aiida_gromacs.parsers.genion aiida_gromacs.parsers.grompp aiida_gromacs.parsers.make_ndx aiida_gromacs.parsers.mdrun aiida_gromacs.parsers.pdb2gmx aiida_gromacs.parsers.solvate aiida_gromacs.workflows aiida_gromacs.workflows.simsetup

N

nptequilibrate() (aiida_gromacs.workflows.simsetup.SetupWorkChain method)

nvtequilibrate() (aiida_gromacs.workflows.simsetup.SetupWorkChain method)

O

outfile_list (aiida_gromacs.data.plumed_input.PlumedInputData property)

output_parsed_metadata() (aiida_gromacs.parsers.mdrun.MdrunParser method)

P

parse() (aiida_gromacs.parsers.editconf.EditconfParser method) (aiida_gromacs.parsers.genericMD.GenericParser method) (aiida_gromacs.parsers.genion.GenionParser method) (aiida_gromacs.parsers.grompp.GromppParser method) (aiida_gromacs.parsers.make_ndx.Make_ndxParser method) (aiida_gromacs.parsers.mdrun.MdrunParser method) (aiida_gromacs.parsers.pdb2gmx.Pdb2gmxParser method) (aiida_gromacs.parsers.solvate.SolvateParser method) parse_file_contents() (aiida_gromacs.parsers.mdrun.MdrunParser method) parse_plumed_input_file() (in module aiida_gromacs.data.plumed_input) pdb2gmx() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) Pdb2gmxCalculation (class in aiida_gromacs.calculations.pdb2gmx)

Pdb2gmxParameters (class in aiida_gromacs.data.pdb2gmx) Pdb2gmxParser (class in aiida_gromacs.parsers.pdb2gmx) PlumedInputData (class in aiida_gromacs.data.plumed_input) populate_plumed_files_to_inputs() (in module aiida_gromacs.data.plumed_input) prepare_for_submission() (aiida_gromacs.calculations.editconf.EditconfCalculation method) (aiida_gromacs.calculations.genericMD.GenericCalculation method) (aiida_gromacs.calculations.genion.GenionCalculation method) (aiida_gromacs.calculations.grompp.GromppCalculation method) (aiida_gromacs.calculations.make_ndx.Make_ndxCalculation method) (aiida_gromacs.calculations.mdrun.MdrunCalculation method) (aiida_gromacs.calculations.pdb2gmx.Pdb2gmxCalculation method) (aiida_gromacs.calculations.solvate.SolvateCalculation method) prodmd() (aiida_gromacs.workflows.simsetup.SetupWorkChain method)

R

result() (aiida_gromacs.workflows.simsetup.SetupWorkChain method)

S

schema (aiida_gromacs.data.editconf.EditconfParameters attribute) (aiida_gromacs.data.genion.GenionParameters attribute) (aiida_gromacs.data.grompp.GromppParameters attribute) (aiida_gromacs.data.make_ndx.Make_ndxParameters attribute) (aiida_gromacs.data.mdrun.MdrunParameters attribute) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters attribute) (aiida_gromacs.data.solvate.SolvateParameters attribute)

set_file() (aiida_gromacs.data.plumed_input.PlumedInputData method) setup_generic_code() (in module aiida_gromacs.helpers) SetupWorkChain (class in aiida_gromacs.workflows.simsetup) solvate() (aiida_gromacs.workflows.simsetup.SetupWorkChain method) SolvateCalculation (class in aiida_gromacs.calculations.solvate) SolvateParameters (class in aiida_gromacs.data.solvate) SolvateParser (class in aiida_gromacs.parsers.solvate)

V

validate() (aiida_gromacs.data.editconf.EditconfParameters method) (aiida_gromacs.data.genion.GenionParameters method) (aiida_gromacs.data.grompp.GromppParameters method) (aiida_gromacs.data.make_ndx.Make_ndxParameters method) (aiida_gromacs.data.mdrun.MdrunParameters method) (aiida_gromacs.data.pdb2gmx.Pdb2gmxParameters method) (aiida_gromacs.data.solvate.SolvateParameters method)