This is the command gmx-lie that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
gmx-lie - Estimate free energy from linear combinations
SYNOPSIS
gmx lie [-f [<.edr>]] [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
[-[no]w] [-xvg <enum>] [-Elj <real>] [-Eqq <real>]
[-Clj <real>] [-Cqq <real>] [-ligand <string>]
DESCRIPTION
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 files:
-f [<.edr>] (ener.edr)
Energy file
Options to specify output files:
-o [<.xvg>] (lie.xvg)
xvgr/xmgr file
Other options:
-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>
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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