GMX-GENION(1)

✨ GMX-GENION ✨

okay bestie, welcome to gmx-genion 💖 this is the GROMACS one, and she is the girl for sprinkling ions into your simulation box like glitter on a craft project ✨

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🌸 NAME 🌸

gmx-genion — generate monoatomic ions on energetically favorable positions 🧚

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🎀 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]

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💅 DESCRIPTION 💅

so what she does is: gmx genion randomly replaces solvent molecules with monoatomic ions 🔥 random, but make it science.

the group of solvent molecules you pick has to be continuous and every single molecule in it has to have the same number of atoms — no chaotic mixed bags, bestie, she can't work with that 😭

then you gotta add the ion molecules to your topology file yourself, OR let the -p option do it for you automatically 🫶

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the naming lore, pay attention 👑

the ion molecule type, residue and atom names in all force fields are the capitalized element names without sign. this molecule name is what you hand over with -pname or -nname, and then the [molecules] section of your topology gets updated accordingly — either by hand or with -p.

⚠️ do NOT use an atom name instead, bestie. that is not the vibe. 💀

ions that can have multiple charge states get the multiplicity added, without sign, for the uncommon states only ✨

and for the bigger ions — like sulfate, for example — we recommend using gmx insert-molecules instead 🙈

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✨ OPTIONS ✨

🦋 Options to specify input files 🦋

• -s [<.tpr>] (topol.tpr) — portable xdr run input file, aka the whole blueprint of your run 💜
• -n [<.ndx>] (index.ndx) (Optional) — index file, if you have one 🎀

🌈 Options to specify input/output files 🌈

• -p [<.top>] (topol.top) (Optional) — topology file, she reads it and edits it, main character energy 👑

🍓 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 and non-solvent 🎀
• -seed <int> (0) — seed for random number generator (0 means generate) 🎲
• -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 ⚖️

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💀 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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🌟 SEE ALSO 🌟

• gmx(1)

more information about GROMACS is available at <http://www.gromacs.org/> 🌈

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👑 COPYRIGHT 👑

2026, GROMACS development team 💖

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and that's the whole page, bestie 🫶 this was GROMACS 2026.4, dated Oct 02, 2026 — go ionize something iconic 💅✨