.TH g_lie 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_lie - free energy estimate from linear combinations

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_lie\fP
.BI "\-f" " ener.edr "
.BI "\-o" " lie.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-Elj" " real "
.BI "\-Eqq" " real "
.BI "\-Clj" " real "
.BI "\-Cqq" " real "
.BI "\-ligand" " string "
.SH DESCRIPTION
\&\fB g_lie\fR 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.
.SH FILES
.BI "\-f" " ener.edr" 
.B Input
 Energy file 

.BI "\-o" " lie.xvg" 
.B Output
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-Elj"  " real" " 0     " 
 Lennard\-Jones interaction between ligand and solvent

.BI "\-Eqq"  " real" " 0     " 
 Coulomb interaction between ligand and solvent

.BI "\-Clj"  " real" " 0.181 " 
 Factor in the LIE equation for Lennard\-Jones component of energy

.BI "\-Cqq"  " real" " 0.5   " 
 Factor in the LIE equation for Coulomb component of energy

.BI "\-ligand"  " string" " none" 
 Name of the ligand in the energy file

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.