Manual:genion 3.3.2

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Contents 1 Description 2 Known Problems 3 Files 4 Options

[edit] 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.

[edit] 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.

[edit] Files

Option     Filename     Type         Description
-----------------------------------------------------
-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
-p         topol.top    In/Out, Opt. Topology file

[edit] Options

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-nice        int    19      Set the nicelevel
-[no]xvgr    bool   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          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]random  bool   yes     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]neutral bool   no      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.