gmx mdmat¶
Synopsis¶
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>]
Description¶
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