NAME

       g_enemat - extracts an energy matrix from an energy file

       VERSION 4.6.5

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]coulsr -[no]coullr -[no]coul14 -[no]ljsr -[no]ljlr -[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 = E_0 + kT log(exp((E-E_0)/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]coulsryes
        extract Coulomb SR energies

       -[no]coullrno
        extract Coulomb LR energies

       -[no]coul14no
        extract Coulomb 1-4 energies

       -[no]ljsryes
        extract Lennard-Jones SR energies

       -[no]ljlrno
        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 2 Dec 2013                                      g_enemat(1)