gmx-lie (1)

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>]

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 to specify input and output files:

-f [<.edr>] (ener.edr) (Input)

    Energy file

-o [<.xvg>] (lie.xvg) (Output)

    xvgr/xmgr file

Other options:

-nice <int> (19)

    Set the nicelevel

-b <time> (0)

    First frame (ps) to read from trajectory

-e <time> (0)

    Last frame (ps) to read from trajectory

-dt <time> (0)

    Only use frame when t MOD dt = first time (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

gromacs(7)

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