g_lie(1) - Linux man page

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