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gmx-lie - Estimate free energy from linear combinations


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>]


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)

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 files:

-f [<.edr>] (ener.edr)
Energy file

Options to specify output files:

-o [<.xvg>] (lie.xvg)
xvgr/xmgr file

Other options:

-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>
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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