g_lie (1) - Linux Manuals

g_lie: free energy estimate from linear combinations

NAME

g_lie - free energy estimate from linear combinations

VERSION 4.0.1

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) LJ-SR (A-B) etc.

FILES

-f ener.edr Input
 Energy file: edr ene 

-o lie.xvg Output
 xvgr/xmgr file 

OTHER OPTIONS

-[no]hno
 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]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 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