Provided by: gromacs-data_4.6.5-1build1_all bug


       g_enemat - extracts an energy matrix from an energy file

       VERSION 4.6.5


       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


        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:




       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.


       -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


        Print help info and quit

        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)

        View output  .xvg,  .xpm,  .eps and  .pdb files

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

        Sum the energy terms selected rather than display them all

       -skip int 0
        Skip number of frames between data points

        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

        extract Coulomb SR energies

        extract Coulomb LR energies

        extract Coulomb 1-4 energies

        extract Lennard-Jones SR energies

        extract Lennard-Jones LR energies

        extract Lennard-Jones 1-4 energies

        extract Buckingham SR energies

        extract Buckingham LR energies

        calculate free energy

       -temp real 300
        reference temperature for free energy calculation



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                              g_enemat(1)