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 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.