gmx-lie man page on DragonFly

gmx-lie man page on DragonFly

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gmx-lie(1)			GROMACS Manual			    gmx-lie(1)

NAME
       gmx-lie - Estimate free energy from linear combinations

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 val‐
       ues 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.gro‐
       macs.org/>.

VERSION 5.0.6							    gmx-lie(1)

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