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)