Man page - gmx-lie(1)
Packages contains this manual
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- gmx-energy(1)
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apt-get install gromacs-data
Manual
GMX-LIE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
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)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit 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
SEE ALSO
gmx(1)
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2025, GROMACS development team