g_lie1
Estimate free energy from linear combinations
Part of gmx-lie(1).
Usage
gmx lie
[-f
[<.edr>]]
[-o
[<.xvg>]]
[-nice
<int>]
[-b
<time>]
[-e
<time>]
[-dt
<time>]
[-
[no]
w]
[-xvg
<enum>]
[-Elj
<real>]
[-Eqq
<real>]
[-Clj
<real>]
[-Cqq
<real>]
[-ligand
<string>]
Overview
gmx lie computes a free energy estimate based on an energy analysis from nonbonded energies. One needs an energy file with the following components: Coul-(A-B) LJ-SR (A-B) etc.
To utilize g_lie correctly, two simulations are required: one with the molecule of interest bound to its receptor and one with the molecule in water. Both need to utilize energygrps such that Coul-SR(A-B), LJ-SR(A-B), etc. terms are written to the .edr file. Values from the molecule-in-water simulation are necessary for supplying suitable values for -Elj and -Eqq.
Options
Options to specify input and output files:
-f [<.edr>] (ener.edr) (Input)
Energy file
-o [<.xvg>] (lie.xvg) (Output)
xvgr/xmgr file
Other options:
-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
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, 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
-ligand <string> (none)
Name of the ligand in the energy file
Releases
5 releases since Debian 4.0 (Etch); the text changed 4 times.