1GMX-LIE(1)                          GROMACS                         GMX-LIE(1)
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NAME

6       gmx-lie - Estimate free energy from linear combinations
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SYNOPSIS

9          gmx lie [-f [<.edr>]] [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
10                  [-[no]w] [-xvg <enum>] [-Elj <real>] [-Eqq <real>]
11                  [-Clj <real>] [-Cqq <real>] [-ligand <string>]
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DESCRIPTION

14       gmx  lie  computes  a  free energy estimate based on an energy analysis
15       from nonbonded energies. One needs an energy file  with  the  following
16       components: Coul-(A-B) LJ-SR (A-B) etc.
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18       To  utilize g_lie correctly, two simulations are required: one with the
19       molecule of interest bound to its receptor and one with the molecule in
20       water.   Both  need  to  utilize  energygrps  such  that  Coul-SR(A-B),
21       LJ-SR(A-B), etc. terms are written to the .edr file.  Values  from  the
22       molecule-in-water  simulation are necessary for supplying suitable val‐
23       ues for -Elj and -Eqq.
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OPTIONS

26       Options to specify input files:
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28       -f [<.edr>] (ener.edr)
29              Energy file
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31       Options to specify output files:
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33       -o [<.xvg>] (lie.xvg)
34              xvgr/xmgr file
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36       Other options:
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38       -b <time> (0)
39              Time of first frame to read from trajectory (default unit ps)
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41       -e <time> (0)
42              Time of last frame to read from trajectory (default unit ps)
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44       -dt <time> (0)
45              Only use frame when t MOD dt = first time (default unit ps)
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47       -[no]w (no)
48              View output .xvg, .xpm, .eps and .pdb files
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50       -xvg <enum> (xmgrace)
51              xvg plot formatting: xmgrace, xmgr, none
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53       -Elj <real> (0)
54              Lennard-Jones interaction between ligand and solvent
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56       -Eqq <real> (0)
57              Coulomb interaction between ligand and solvent
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59       -Clj <real> (0.181)
60              Factor in the LIE equation for Lennard-Jones component of energy
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62       -Cqq <real> (0.5)
63              Factor in the LIE equation for Coulomb component of energy
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65       -ligand <string> (none)
66              Name of the ligand in the energy file
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SEE ALSO

69       gmx(1)
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71       More    information    about    GROMACS    is    available    at     <‐
72       http://www.gromacs.org/>.
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75       2022, GROMACS development team
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802022.2                           Jun 16, 2022                       GMX-LIE(1)
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