g_enemat(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				       g_enemat(1)

NAME

       g_enemat - extracts an energy matrix from an energy file

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_enemat  -f  ener.edr  -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -[no]version -nice int -b time -e time -dt
       time -[no]w -xvg enum -[no]sum -skip int -[no]mean -nlevels int -max real  -min	real  -[no]coul  -[no]coulr  -[no]coul14  -[no]lj  -[no]lj
       -[no]lj14 -[no]bhamsr -[no]bhamlr -[no]free -temp real

DESCRIPTION

	 g_enemat  extracts an energy matrix from the energy file ( -f).  With	-groups a file must be supplied with on each line a group of atoms
       to be used. For these groups matrix of interaction energies will be extracted from the energy file by looking for energy groups with  names
       corresponding to pairs of groups of atoms, e.g. if your	-groups file contains:

	2

	Protein

	SOL

       then  energy  groups with names like 'Coul-SR:Protein-SOL' and 'LJ:Protein-SOL' are expected in the energy file (although  g_enemat is most
       useful if many groups are analyzed simultaneously). Matrices for different energy types are written out separately, as controlled by  the
       -[no]coul,   -[no]coulr,   -[no]coul14,	  -[no]lj,   -[no]lj14,   -[no]bham and  -[no]free options.  Finally, the total interaction energy
       energy per group can be calculated ( -etot).

       An approximation of the free energy can be calculated using: E(free) = E0 + kT log( exp((E-E0)/kT) ), where '' stands for  time-average.  A
       file  with  reference  free  energies  can be supplied to calculate the free energy difference with some reference state. Group names (e.g.
       residue names) in the reference file should correspond to the group names as used in the  -groups file, but a appended number (e.g. residue
       number) in the  -groups will be ignored in the comparison.

FILES

       -f ener.edr Input, Opt.
	Energy file

       -groups groups.dat Input
	Generic data file

       -eref eref.dat Input, Opt.
	Generic data file

       -emat emat.xpm Output
	X PixMap compatible matrix file

       -etot energy.xvg Output
	xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -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]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]sumno
	Sum the energy terms selected rather than display them all

       -skip int 0
	Skip number of frames between data points

       -[no]meanyes
	with  -groups extracts matrix of mean energies instead of matrix for each timestep

       -nlevels int 20
	number of levels for matrix colors

       -max real 1e+20
	max value for energies

       -min real -1e+20
	min value for energies

       -[no]coulyes
	extract Coulomb SR energies

       -[no]coulrno
	extract Coulomb LR energies

       -[no]coul14no
	extract Coulomb 1-4 energies

       -[no]ljyes
	extract Lennard-Jones SR energies

       -[no]ljno
	extract Lennard-Jones LR energies

       -[no]lj14no
	extract Lennard-Jones 1-4 energies

       -[no]bhamsrno
	extract Buckingham SR energies

       -[no]bhamlrno
	extract Buckingham LR energies

       -[no]freeyes
	calculate free energy

       -temp real 300
	reference temperature for free energy calculation

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011						       g_enemat(1)