g_lie(1)
NAME
g_lie - free energy estimate from linear combinations
SYNOPSIS
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
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) LJSR (A-B) etc.
FILES
- -f ener.edr Input
- Generic energy: edr ene
- -o lie.xvg Output
- xvgr/xmgr file
OTHER OPTIONS
- -[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
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.