table of contents
genion(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | genion(1) |
NAME¶
genion - generates mono atomic ions on energetically favorable positionsSYNOPSIS¶
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]neutralDESCRIPTION¶
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.FILES¶
-s topol.tpr InputRun input file: tpr tpb tpa
xvgr/xmgr file
Index file
Structure file: gro g96 pdb etc.
Log file
Protein data bank file
Topology file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
xvg plot formatting: xmgrace, xmgr or none
Number of positive ions
Name of the positive ion
Charge of the positive ion
Number of negative ions
Name of the negative ion
Charge of the negative ion
Minimum distance between ions
Use random placement of ions instead of based on potential. The rmin option should still work
Seed for random number generator
Scaling factor for the potential for -pot
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.
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.SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |