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gmx-genion - Online in the Cloud

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This is the command gmx-genion that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-genion - Generate monoatomic ions on energetically favorable positions

SYNOPSIS


gmx genion [-s [<.tpr>]] [-n [<.ndx>]] [-p [<.top>]]
[-o [<.gro/.g96/...>]] [-np <int>] [-pname <string>]
[-pq <int>] [-nn <int>] [-nname <string>] [-nq <int>]
[-rmin <real>] [-seed <int>] [-conc <real>] [-[no]neutral]

DESCRIPTION


gmx 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 gmx insert-molecules.

OPTIONS


Options to specify input files:

-s [<.tpr>] (topol.tpr)
Portable xdr run input file

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify input/output files:

-p [<.top>] (topol.top) (Optional)
Topology file

Options to specify output files:

-o [<.gro/.g96/...>] (out.gro)
Structure file: gro g96 pdb brk ent esp

Other options:

-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 (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 ISSUES


· 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.

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