---
name: "gmx-lie"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-lie"
---

# gmx-lie(1)

Estimate free energy from linear combinations

## NAME

gmx-lie - Estimate free energy from linear combinations

## 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>]
```

## DESCRIPTION

**gmx lie** computes a free energy estimate based on an energy analysis from nonbonded energies. One needs an energy file with the following components: Coul-(A-B) LJ-SR (A-B) etc.

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. Both need to utilize **energygrps** such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the *.edr* file. Values from the molecule-in-water simulation are necessary for supplying suitable values for -Elj and -Eqq.

## OPTIONS

Options to specify input files:

- **-f \[\<.edr\>\] (ener.edr)**

  Energy file

Options to specify output files:

- **-o \[\<.xvg\>\] (lie.xvg)**

  xvgr/xmgr file

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

- **-xvg \<enum\> (xmgrace)**

  xvg plot formatting: xmgrace, xmgr, none

- **-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

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team