gmx-mdmat1
Calculate residue contact maps
Usage
gmx mdmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[-mean [<.xpm>]] [-frames [<.xpm>]] [-no [<.xvg>]]
[-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
[-t <real>] [-nlevels <int>]
Overview
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
Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
|
Trajectory: xtc trr cpt gro g96 pdb tng |
|---|---|
-s [<.tpr/.gro/...>] (topol.tpr)
|
Structure+mass(db): tpr gro g96 pdb brk ent |
-n [<.ndx>] (index.ndx) (Optional)
|
Index file |
Options to specify output files:
-mean [<.xpm>] (dm.xpm)
|
X PixMap compatible matrix file |
|---|---|
-frames [<.xpm>] (dmf.xpm) (Optional)
|
X PixMap compatible matrix file |
-no [<.xvg>] (num.xvg) (Optional)
|
xvgr/xmgr file |
Other options:
-b <time> (0)
|
Time of first frame to read from trajectory (default unit ps) |
|---|---|
-e <time> (0)
|
Time of last frame to read from trajectory (default unit ps) |
-dt <time> (0)
|
Only use frame when t MOD dt = first time (default unit 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 |
Releases
6 releases since Debian 8 (Jessie); the text changed 5 times.