gmx lie

Main Table of Contents VERSION 5.0-rc1-20140407-49a43a6-dirty

Synopsis

gmx lie [-f [<.edr>]] [-o [<.xvg>]] [-nice ] [-b 

Description

gmx 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.

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


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