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/>.