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)

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COPYRIGHT

       2020, GROMACS development team