Provided by: gromacs-data_2019.1-1_all bug


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


          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]coul14] [-[no]ljsr]
                     [-[no]lj14] [-[no]bhamsr] [-[no]free] [-temp <real>]


       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:


       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 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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

       -[no]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum> (xmgrace)
              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]coul14 (no)
              extract Coulomb 1-4 energies

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

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

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

       -[no]free (yes)
              calculate free energy

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



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       2019, GROMACS development team