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LEARN ABOUT DEBIAN

g_lie

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)

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