---
name: "g_lie_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-lie"
---

# g\_lie\_d(1)

Estimate free energy from linear combinations

Part of [gmx-lie(1)](/gmx-lie/1.md).

## NAME

gmx-lie - Estimate free energy from linear combinations

## SYNOPSIS

gmx lie \[-f \[\<.edr\>\]\] \[-o \[\<.xvg\>\]\] \[-nice \<int\>\] \[-b \<time\>\]\
         \[-e \<time\>\] \[-dt \<time\>\] \[-\[no\]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 and output files:

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

**-o** *\[\<.xvg\>\] (lie.xvg) (Output)*\
     xvgr/xmgr file

Other options:

**-nice** *\<int\> (19)*\
     Set the nicelevel

**-b** *\<time\> (0)*\
     First frame (ps) to read from trajectory

**-e** *\<time\> (0)*\
     Last frame (ps) to read from trajectory

**-dt** *\<time\> (0)*\
     Only use frame when t MOD dt = first time (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

**[gromacs(7)](/gromacs/7.md)**

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