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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

       2019, GROMACS development team