GMX-LIE(1)

💖 GMX-LIE(1) — the GROMACS manual page, but make it make sense 💖

okay bestie, we're in the GROMACS section of the manual and today's main character is gmx-lie. pull up a chair, grab a strawberry 🍓, and let's get into it.

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✨ NAME ✨

gmx-lie — Estimate free energy from linear combinations

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🌸 SYNOPSIS 🌸

gmx lie [-f [<.edr>]] [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
        [-[no]w] [-xvg <enum>] [-Elj <real>] [-Eqq <real>]
        [-Clj <real>] [-Cqq <real>] [-ligand <string>]

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🦋 DESCRIPTION 🦋

so gmx lie computes a free energy estimate based on an energy analysis from nonbonded energies. that's the whole vibe. lowkey iconic, highkey specific.

to make it work you need an energy file with the following components: Coul-(A-B) LJ-SR (A-B) etc. like, those exact terms, no substitutions, this is not a make-it-up situation 💅

to utilize g_lie correctly, two simulations are required: one with the molecule of interest bound to its receptor, and one with the molecule in water. bestie you need both, this is a two-simulation kinda deal, no shortcuts 🙈

both of them need to utilize energygrps such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the .edr file. if they're not in there, the whole thing's giving nothing. 😭

and the values from the molecule-in-water simulation are necessary for supplying suitable values for -Elj and -Eqq. so like, that water sim isn't decorative, she's load-bearing.

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🎀 OPTIONS 🎀

💾 Options to specify input files:

• -f [<.edr>] (ener.edr) — Energy file. the whole energy situation lives here, bestie.

📤 Options to specify output files:

• -o [<.xvg>] (lie.xvg) — xvgr/xmgr file. this is where your pretty plot goes ✨

⭐ Other options:

• -b <time> (0) — Time of first frame to read from trajectory (default unit ps)
• -e <time> (0) — Time of last frame to read from trajectory (default unit ps)
• -dt <time> (0) — Only use frame when t MOD dt = first time (default unit ps)
• -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files. flip it on if you want the visuals, you know you do 👀
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none. pick your aesthetic, it's giving choose-your-own-plot-format 🌈
• -Elj <real> (0) — Lennard-Jones interaction between ligand and solvent
• -Eqq <real> (0) — Coulomb interaction between ligand and solvent
• -Clj <real> (0.181) — Factor in the LIE equation for Lennard-Jones component of energy
• -Cqq <real> (0.5) — Factor in the LIE equation for Coulomb component of energy
• -ligand <string> (none) — Name of the ligand in the energy file. tell it who the girl is, she can't guess 🫶

no cap: -Elj and -Eqq defaults are 0, but the description literally says you need molecule-in-water values for those. so like, don't just roll with the defaults and act surprised, okay? 😭

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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 thing, bestie, you ate 🍽️✨ periodt

this was GMX-LIE(1) from the GROMACS manual, version 2026.4, dated Oct 02, 2026 — mwah, go run your simulations 💅💖🦋