1 .TH g_lie 1 "Fri 19 Apr 2013" "" "GROMACS suite, VERSION 4.5.7"
3 g_lie - free energy estimate from linear combinations
11 .BI "\-[no]version" ""
22 .BI "\-ligand" " string "
24 \&\fB g_lie\fR computes a free energy estimate based on an energy analysis
25 \&from. One needs an energy file with the following components:
26 \&Coul (A\-B) LJ\-SR (A\-B) etc.
38 Print help info and quit
40 .BI "\-[no]version" "no "
41 Print version info and quit
43 .BI "\-nice" " int" " 19"
46 .BI "\-b" " time" " 0 "
47 First frame (ps) to read from trajectory
49 .BI "\-e" " time" " 0 "
50 Last frame (ps) to read from trajectory
52 .BI "\-dt" " time" " 0 "
53 Only use frame when t MOD dt = first time (ps)
56 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
58 .BI "\-xvg" " enum" " xmgrace"
59 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
61 .BI "\-Elj" " real" " 0 "
62 Lennard\-Jones interaction between ligand and solvent
64 .BI "\-Eqq" " real" " 0 "
65 Coulomb interaction between ligand and solvent
67 .BI "\-Clj" " real" " 0.181 "
68 Factor in the LIE equation for Lennard\-Jones component of energy
70 .BI "\-Cqq" " real" " 0.5 "
71 Factor in the LIE equation for Coulomb component of energy
73 .BI "\-ligand" " string" " none"
74 Name of the ligand in the energy file
79 More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.