Index

A

append_ligand() (in module gromacs_extra.append_ligand)

AppendLigand (class in gromacs_extra.append_ligand)

C

check_lengths() (gromacs.pdb2gmx.Pdb2gmx method)

convert_tpr() (in module gromacs.convert_tpr) ConvertTpr (class in gromacs.convert_tpr)

E

Editconf (class in gromacs.editconf)

editconf() (in module gromacs.editconf)

F

find_length() (gromacs.pdb2gmx.Pdb2gmx method)

G

Genion (class in gromacs.genion) genion() (in module gromacs.genion) Genrestr (class in gromacs.genrestr) genrestr() (in module gromacs.genrestr) Gmxselect (class in gromacs.gmxselect) gmxselect() (in module gromacs.gmxselect) gromacs.convert_tpr module gromacs.editconf module gromacs.genion module gromacs.genrestr module gromacs.gmxselect module gromacs.grompp module gromacs.grompp_mdrun module

gromacs.make_ndx module gromacs.mdrun module gromacs.mdrun_plumed module gromacs.pdb2gmx module gromacs.solvate module gromacs.trjcat module gromacs_extra.append_ligand module gromacs_extra.ndx2resttop module Grompp (class in gromacs.grompp) grompp() (in module gromacs.grompp) grompp_mdrun() (in module gromacs.grompp_mdrun) GromppMdrun (class in gromacs.grompp_mdrun)

L

launch() (gromacs.convert_tpr.ConvertTpr method) (gromacs.editconf.Editconf method) (gromacs.genion.Genion method) (gromacs.genrestr.Genrestr method) (gromacs.gmxselect.Gmxselect method) (gromacs.grompp.Grompp method) (gromacs.grompp_mdrun.GromppMdrun method) (gromacs.make_ndx.MakeNdx method) (gromacs.mdrun.Mdrun method) (gromacs.mdrun_plumed.MdrunPlumed method) (gromacs.pdb2gmx.Pdb2gmx method) (gromacs.solvate.Solvate method) (gromacs.trjcat.Trjcat method) (gromacs_extra.append_ligand.AppendLigand method) (gromacs_extra.ndx2resttop.Ndx2resttop method)

M

make_ndx() (in module gromacs.make_ndx) MakeNdx (class in gromacs.make_ndx) Mdrun (class in gromacs.mdrun) mdrun() (in module gromacs.mdrun) mdrun_plumed() (in module gromacs.mdrun_plumed) MdrunPlumed (class in gromacs.mdrun_plumed) module gromacs.convert_tpr gromacs.editconf gromacs.genion gromacs.genrestr gromacs.gmxselect gromacs.grompp gromacs.grompp_mdrun gromacs.make_ndx gromacs.mdrun gromacs.mdrun_plumed gromacs.pdb2gmx gromacs.solvate gromacs.trjcat gromacs_extra.append_ligand gromacs_extra.ndx2resttop

N

Ndx2resttop (class in gromacs_extra.ndx2resttop)

ndx2resttop() (in module gromacs_extra.ndx2resttop)

P

Pdb2gmx (class in gromacs.pdb2gmx)

pdb2gmx() (in module gromacs.pdb2gmx)

S

Solvate (class in gromacs.solvate)

solvate() (in module gromacs.solvate) stage_files() (gromacs.mdrun_plumed.MdrunPlumed method)

T

Trjcat (class in gromacs.trjcat)

trjcat() (in module gromacs.trjcat)