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Man Pages


Manual Reference Pages  -  GMX-LIE (1)

NAME

gmx-lie - Estimate free energy from linear combinations

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

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>]

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 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

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.

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VERSION 5.0.6 GMX-LIE (1)

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