gmx-genion man page

gmx-genion — Generate monoatomic ions on energetically favorable positions

Synopsis

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]

Description

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

Options to specify input files:

-s [<.tpr>] (topol.tpr)
Portable xdr run input file
-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify input/output files:

-p [<.top>] (topol.top) (Optional)
Topology file

Options to specify output files:

-o [<.gro/.g96/...>] (out.gro)
Structure file: gro g96 pdb brk ent esp

Other options:

-np <int> (0)
Number of positive ions
-pname <string> (NA)
Name of the positive ion
-pq <int> (1)
Charge of the positive ion
-nn <int> (0)
Number of negative ions
-nname <string> (CL)
Name of the negative ion
-nq <int> (-1)
Charge of the negative ion
-rmin <real> (0.6)
Minimum distance between ions
-seed <int> (0)
Seed for random number generator (0 means generate)
-conc <real> (0)
Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input .tpr file. Overrides the -np and -nn options.
-[no]neutral (no)
This option will add enough ions to neutralize the system. These ions are added on top of those specified with -np/-nn or -conc.

Known Issues

·
If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added.

See Also

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

Referenced By

gmx(1).

Oct 28, 2016 2016.1 GROMACS