Provided by: gromacs-data_2023.3-1ubuntu3_all bug

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)

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


COPYRIGHT
       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                        GMX-LIE(1)