NAME
genion - generates mono atomic ions on energetically favorable
positions
VERSION 4.0.1
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 -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
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 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
option.
For larger ions, e.g. sulfate we recommended to use 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
-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
-nice int 19
Set the nicelevel
-[no]xvgryes
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
-[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 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. 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/>.
Thu 16 Oct 2008 genion(1)