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.
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:
Options to specify output files:
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)
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