g_lie − free energy estimate from linear combinations
g_lie -f ener.edr -o lie.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -Elj real -Eqq real -Clj real -Cqq real -ligand string
g_lie computes a free energy estimate based on an energy analysis from. One needs an energy file with the following components: Coul (A-B) LJ-SR (A-B) etc.
-f ener.edr Input
Generic energy: edr ene
-o lie.xvg Output
xvgr/xmgr file
-[no]h no
Print help info and quit
-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
-[no]xvgr yes
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-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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