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       genion   -  generates  mono  atomic  ions  on  energetically  favorable

       VERSION 4.0.1


       genion -s  topol.tpr  -table  table.xvg  -n  index.ndx  -o  out.gro  -g
       genion.log -pot pot.pdb -p -[no]h -nice int -[no]xvgr -np int
       -pname string -pq  int  -nn  int  -nname  string  -nq  int  -rmin  real
       -[no]random -seed int -scale real -conc real -[no]neutral


       genion replaces solvent molecules by monoatomic ions at the position of
       the first atoms with the most favorable electrostatic potential  or  at
       random.  The potential is calculated on all atoms, using normal GROMACS
       particle based methods (in contrast to other methods based  on  solving
       the  Poisson-Boltzmann  equation).  The potential is recalculated after
       every ion insertion.  If specified in the run input  file,  a  reaction
       field,  shift  function  or  user  function  can  be used. For the user
       function a table file can be specified with the  option   -table.   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 and include the file  ions.itp.  Ion
       names for Gromos96 should include the charge.

       With the option  -pot the potential can be written as  B-factors  in  a
       pdb  file  (for  visualisation  using  e.g.  rasmol).   The unit of the
       potential is 1000 kJ/(mol e), the scaling be changed with  the   -scale

       For larger ions, e.g. sulfate we recommended to use genbox.


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

       -table table.xvg Input, Opt.
        xvgr/xmgr file

       -n index.ndx Input, Opt.
        Index file

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

       -g genion.log Output
        Log file

       -pot pot.pdb Output, Opt.
        Protein data bank file

       -p In/Out, Opt.
        Topology file


        Print help info and quit

       -nice int 19
        Set the nicelevel

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -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

        Use random placement of ions instead of based on potential.  The  rmin
       option should still work

       -seed int 1993
        Seed for random number generator

       -scale real 0.001
        Scaling factor for the potential for -pot

       -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.

        This  option  will  add  enough  ions  to  neutralize  the  system. In
       combination with the concentration option a neutral system at  a  given
       salt concentration will be generated.


       -  Calculation of the potential is not reliable, therefore the  -random
       option is now turned on by default.

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



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                      genion(1)