SYNOPSIS
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 intDESCRIPTION
g_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 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 InputTrajectory: 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]hnoPrint help info and quit
-[no]versionno
Print version 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)
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-t real 1.5
trunc distance
-nlevels int 40
Discretize distance in levels