gmx lie¶
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