gmx-lie - Estimate free energy from linear combinations

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                        GMX-LIE(1)

gmxlie 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.

       gmx-lie - Estimate free energy from linear combinations

       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

gmx(1)

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

          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>]