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)-s[<.tpr/.gro/…>] (topol.tpr)-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