g_lie(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_lie(1)
NAME
g_lie - free energy estimate from linear combinations
VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_lie -f ener.edr -o lie.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -Elj real -Eqq real -Clj real -Cqq
real -ligand string
DESCRIPTION
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.
FILES
-f ener.edr Input
Energy file
-o lie.xvg Output
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
Print help info and quit
-[no]versionno
Print version 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]wno
View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or 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
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_lie(1)
