| 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 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¶
More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT¶
2024, GROMACS development team
| August 29, 2024 | 2024.3 |