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GMX-ENEMAT(1)			    GROMACS			 GMX-ENEMAT(1)

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]coul14] [-[no]ljsr]
		     [-[no]lj14] [-[no]bhamsr] [-[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 ex-
       tracted 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 aCoul-SR:Protein-SOLa	 and  aLJ:Pro-
       tein-SOLa  are expected in the energy file (although gmx	enemat is most
       useful if many groups are analyzed simultaneously). Matrices  for  dif-
       ferent  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 a<>a 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)
	      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

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.4				 Oct 06, 2020			 GMX-ENEMAT(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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