Section: GROMACS suite, VERSION 4.5 (1)Updated: Thu 26 Aug 2010Local indexUp
g_mdmat - calculates residue contact maps
g_mdmat-f traj.xtc -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h-[no]version-nice int -b time -e time -dt time -xvg enum -t real -nlevels int
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.