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GMX-LIE(1) GROMACS GMX-LIE(1)

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) 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 files:

Energy file

Options to specify output files:

xvgr/xmgr file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr, none
Lennard-Jones interaction between ligand and solvent
Coulomb interaction between ligand and solvent
Factor in the LIE equation for Lennard-Jones component of energy
Factor in the LIE equation for Coulomb component of energy
Name of the ligand in the energy file

gmx(1)

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2019, GROMACS development team

February 15, 2019 2019.1