xenial (1) gmx-genion.1.gz

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