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gmx-mdmat(1)			GROMACS	Manual			  gmx-mdmat(1)

NAME
       gmx-mdmat - Calculate residue contact maps

SYNOPSIS
       gmx mdmat [-f [<.xtc/.trr/...>]]	[-s [<.tpr/.tpb/...>]]
		 [-n [<.ndx>]] [-mean [<.xpm>]]	[-frames [<.xpm>]]
		 [-no [<.xvg>]]	[-nice <int>] [-b <time>] [-e <time>]
		 [-dt <time>] [-xvg <enum>] [-t	<real>]	[-nlevels <int>]

DESCRIPTION
       gmx  mdmat  makes distance matrices consisting of the smallest distance
       between residue pairs. With -frames, these  distance  matrices  can  be
       stored  in order	to see differences in tertiary structure as a function
       of time.	If you choose your options unwisely, this may generate a large
       output file. By default,	only an	averaged matrix	over the whole trajec-
       tory is output. Also a count of the number of different atomic contacts
       between	residues over the whole	trajectory can be made.	The output can
       be processed with gmx xpm2ps to make a PostScript (tm) plot.

OPTIONS
       Options to specify input	and output files:

       -f [_.xtc/.trr/..._] (traj.xtc) (Input)
	   Trajectory: xtc trr cpt trj gro g96 pdb tng

       -s [_.tpr/.tpb/..._] (topol.tpr)	(Input)
	   Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

       -n [_.ndx_] (index.ndx) (Input, Optional)
	   Index file

       -mean [_.xpm_] (dm.xpm) (Output)
	   X PixMap compatible matrix file

       -frames [_.xpm_]	(dmf.xpm) (Output, Optional)
	   X PixMap compatible matrix file

       -no [_.xvg_] (num.xvg) (Output, Optional)
	   xvgr/xmgr file

       Other options:

       -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)

       -xvg _enum_ (xmgrace)
	   xvg plot formatting:	xmgrace, xmgr, none

       -t _real_ (1.5)
	   trunc distance

       -nlevels	_int_ (40)
	   Discretize distance in this number of levels

SEE ALSO
       gromacs(7)

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

VERSION	5.0.6							  gmx-mdmat(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO

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