| GMX-GENION(1) | GROMACS | GMX-GENION(1) |
gmx-genion - Generate monoatomic ions on energetically favorable positions
gmx genion [-s [<.tpr>]] [-n [<.ndx>]] [-p [<.top>]]
[-o [<.gro/.g96/...>]] [-np <int>] [-pname <string>]
[-pq <int>] [-nn <int>] [-nname <string>] [-nq <int>]
[-rmin <real>] [-seed <int>] [-conc <real>] [-[no]neutral]
gmx genion randomly replaces solvent molecules with monoatomic ions. The group of solvent molecules should be continuous and all molecules should have the same number of atoms. The user should add the ion molecules to the topology file or use the -p option to automatically modify the topology.
The ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. This molecule name should be given with -pname or -nname, and the [molecules] section of your topology updated accordingly, either by hand or with -p. Do not use an atom name instead!
Ions which can have multiple charge states get the multiplicity added, without sign, for the uncommon states only.
For larger ions, e.g. sulfate we recommended using gmx insert-molecules.
Options to specify input files:
Options to specify input/output files:
Options to specify output files:
Other options:
More information about GROMACS is available at <http://www.gromacs.org/>.
2023, GROMACS development team
| February 3, 2023 | 2022.5 |