NAME

       genion - generates mono atomic ions on energetically favorable positions

       VERSION 4.6.5

SYNOPSIS

       genion  -s  topol.tpr  -n  index.ndx -o out.gro -p topol.top -[no]h -[no]version -nice int -np int -pname
       string -pq int -nn int -nname string -nq int -rmin real -seed int -conc real -[no]neutral

DESCRIPTION

        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  genbox.

FILES

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -n index.ndx Input, Opt.
        Index file

       -o out.gro Output
        Structure file: gro g96 pdb etc.

       -p topol.top In/Out, Opt.
        Topology file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -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]neutralno
        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 PROBLEMS

       -  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

       gromacs(7)

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

                                                 Mon 2 Dec 2013                                        genion(1)