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GMX-LIE(1) GROMACS GMX-LIE(1) 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 val- ues 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) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-LIE(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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