NAME
g_mdmat - calculates residue contact maps
VERSION 4.0.1
SYNOPSIS
g_mdmat -f traj.xtc -s topol.tpr -n index.ndx -mean dm.xpm -frames
dmf.xpm -no num.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr
-t real -nlevels int
DESCRIPTION
g_mdmat makes distance matrices consisting of the smallest distance
between residue pairs. With -frames these distance matrices can be
stored as a function of time, to be able to see differences in tertiary
structure as a funcion of time. If you choose your options unwise, this
may generate a large output file. Default only an averaged matrix over
the whole trajectory 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 xpm2ps to make a
PostScript (tm) plot.
FILES
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt.
Index file
-mean dm.xpm Output
X PixMap compatible matrix file
-frames dmf.xpm Output, Opt.
X PixMap compatible matrix file
-no num.xvg Output, Opt.
xvgr/xmgr file
OTHER OPTIONS
-[no]hno
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)
-[no]xvgryes
Add specific codes (legends etc.) in the output xvg files for the
xmgrace program
-t real 1.5
trunc distance
-nlevels int 40
Discretize distance in levels
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_mdmat(1)