NAME

       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> (1993)
              Seed for random number generator

       -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/>.

COPYRIGHT

       2015, GROMACS development team