.. _gmx lie:

gmx lie
=======

Synopsis
--------

.. parsed-literal::

    gmx lie [:strong:`-f` :emphasis:`[<.edr>]`] [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`]
            [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-Elj` :emphasis:`<real>`] [:strong:`-Eqq` :emphasis:`<real>`]
            [:strong:`-Clj` :emphasis:`<real>`] [:strong:`-Cqq` :emphasis:`<real>`] [:strong:`-ligand` :emphasis:`<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 :ref:`.edr <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 :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <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

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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