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       g_enemat - extracts an energy matrix from an energy file

       VERSION 4.0.1


       g_enemat  -f  ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm
       -etot energy.xvg -[no]h -nice int -b  time  -e  time  -dt  time  -[no]w
       -[no]xvgr -[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


       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




       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.


       -f ener.edr Input, Opt.
        Energy file: edr ene

       -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

       -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

        Add specific codes (legends etc.) in the  output  xvg  files  for  the
       xmgrace program

        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 in stead 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

                                Thu 16 Oct 2008                    g_enemat(1)