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. One needs an energy file with the following components: Coul (A-B) LJ-SR (A-B) etc.
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