.TH gmx-lie 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations

.SH 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>]

.SH DESCRIPTION
\fBgmx lie\fR 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 \fBg_lie\fR 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 \fBenergygrps\fR such that Coul\-SR(A\-B), LJ\-SR(A\-B), etc. terms are written to the \fB.edr\fR file. Values from the molecule\-in\-water simulation are necessary for supplying suitable values for \-Elj and \-Eqq.

.SH OPTIONS
Options to specify input and output files:

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

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


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

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

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

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w" "  (no)"
    View output \fB.xvg\fR, \fB.xpm\fR, \fB.eps\fR and \fB.pdb\fR files

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-Elj" " <real> (0)"
    Lennard\-Jones interaction between ligand and solvent

.BI "\-Eqq" " <real> (0)"
    Coulomb interaction between ligand and solvent

.BI "\-Clj" " <real> (0.181)"
    Factor in the LIE equation for Lennard\-Jones component of energy

.BI "\-Cqq" " <real> (0.5)"
    Factor in the LIE equation for Coulomb component of energy

.BI "\-ligand" " <string> (none)"
    Name of the ligand in the energy file


.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.