gmx lie

	gmx lie
	Main Table of Contents	VERSION 5.0.3

Synopsis

gmx lie [-f [<.edr>]] [-o [<.xvg>]] [-nice ] [-b ] [-e ]
        [-dt ] [-[no]w] [-xvg ] [-Elj ] [-Eqq ]
        [-Clj ] [-Cqq ] [-ligand ]

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 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

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