Main Table of Contents

Fri 5 Jul 2013


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 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.

For larger ions, e.g. sulfate we recommended using genbox.


-s topol.tpr Input Run input file: tpr tpb tpa
-n index.ndx Input, Opt. Index file
-o out.gro Output Structure file: gro g96 pdb etc.
-p In/Out, Opt. Topology file

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-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 bool 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 problems