genion(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 genion(1)

NAME

       genion - generates mono atomic ions on energetically favorable positions

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

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

DESCRIPTION

	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 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.

       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 option.

       For larger ions, e.g. sulfate we recommended using  genbox.

FILES

       -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 etc.

       -g genion.log Output
	Log file

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

       -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

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -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

       -[no]randomyes
	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 vol-
       ume 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. In combination with the concentration option a neutral system at a given salt
       concentration will be generated.

KNOWN PROBLEMS

       - 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
       added.

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							 genion(1)