gmx mdmat

Main Table of Contents VERSION 5.0


gmx mdmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
          [-mean [<.xpm>]] [-frames [<.xpm>]] [-no [<.xvg>]] [-nice ]


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 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 gmx xpm2ps to make a PostScript (tm) plot.


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