genion VERSION 3.3_beta_20050823

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

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.

-s topol.tpr Input Generic run input: tpr tpb tpa xml

-table table.xvg Input, Opt. xvgr/xmgr file

-n index.ndx Input, Opt. Index file

-o out.gro Output Generic structure: gro g96 pdb xml

-g genion.log Output Log file

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

-[no]h no Print help info and quit

-nice int 19 Set the nicelevel

-[no]xvgr yes 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 real 1 Charge of the positive ion

-nn int 0 Number of negative ions

-nname string Cl Name of the negative ion

-nq real -1 Charge of the negative ion

-rmin real 0.6 Minimum distance between ions

-[no]random no 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

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.