NAME

       gmx-enemat - Extract an energy matrix from an energy file

SYNOPSIS

          gmx enemat [-f [<.edr>]] [-groups [<.dat>]] [-eref [<.dat>]]
                     [-emat [<.xpm>]] [-etot [<.xvg>]] [-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

       gmx  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  gmx  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.

OPTIONS

       Options to specify input files:

       -f [<.edr>] (ener.edr) (Optional)
              Energy file

       -groups [<.dat>] (groups.dat)
              Generic data file

       -eref [<.dat>] (eref.dat) (Optional)
              Generic data file

       Options to specify output files:

       -emat [<.xpm>] (emat.xpm)
              X PixMap compatible matrix file

       -etot [<.xvg>] (energy.xvg)
              xvgr/xmgr file

       Other options:

       -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>
              xvg plot formatting: xmgrace, xmgr, none

       -[no]sum (no)
              Sum the energy terms selected rather than display them all

       -skip <int> (0)
              Skip number of frames between data points

       -[no]mean (yes)
              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]coulsr (yes)
              extract Coulomb SR energies

       -[no]coullr (no)
              extract Coulomb LR energies

       -[no]coul14 (no)
              extract Coulomb 1-4 energies

       -[no]ljsr (yes)
              extract Lennard-Jones SR energies

       -[no]ljlr (no)
              extract Lennard-Jones LR energies

       -[no]lj14 (no)
              extract Lennard-Jones 1-4 energies

       -[no]bhamsr (no)
              extract Buckingham SR energies

       -[no]bhamlr (no)
              extract Buckingham LR energies

       -[no]free (yes)
              calculate free energy

       -temp <real> (300)
              reference temperature for free energy calculation

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team

5.1.2                                           February 03, 2016                                  GMX-ENEMAT(1)