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gmx-genion(1)			GROMACS Manual			 gmx-genion(1)

NAME
       gmx-genion  - Generate monoatomic ions on energetically favorable posi‐
       tions

SYNOPSIS
       gmx genion [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
		  [-o [<.gro/.g96/...>]] [-p [<.top>]] [-nice <int>]
		  [-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 mole‐
       cules 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\-mole‐
       cules.

OPTIONS
       Options to specify input and output files:

       -s [<.tpr/.tpb/...>] (topol.tpr) (Input)
	   Run input file: tpr tpb tpa

       -n [<.ndx>] (index.ndx) (Input, Optional)
	   Index file

       -o [<.gro/.g96/...>] (out.gro) (Output)
	   Structure file: gro g96 pdb brk ent esp

       -p [<.top>] (topol.top) (Input/Output, Optional)
	   Topology file

       Other options:

       -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]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
       gromacs(7)

       More  information  about	 GROMACS  is  available	 at   <http://www.gro‐
       macs.org/>.

VERSION 5.0.6							 gmx-genion(1)

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