genion

VERSION 3.1
Thu 28 Feb 2002

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 or shift function can be used. 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.

The potential can be written as B-factors in a pdb file (for visualisation using e.g. rasmol). The unit of the potential is 0.001 kJ/(mol e).

For larger ions, e.g. sulfate we recommended to use genbox.

Files

option	filename	type	description
`-s`	`topol.tpr`	Input	Generic run input: tpr tpb tpa
`-n`	`index.ndx`	Input, Opt.	Index file
`-o`	`out.gro`	Output	Generic structure: gro g96 pdb
`-g`	`genion.log`	Output	Log file
`-pot`	`pot.pdb`	Output, Opt.	Protein data bank file

Other options

option	type	default	description
`-[no]h`	bool	`no`	Print help info and quit
`-[no]X`	bool	`no`	Use dialog box GUI to edit command line options
`-nice`	int	`19`	Set the nicelevel
`-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`	bool	`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

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