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GMX-MDMAT(1) GROMACS GMX-MDMAT(1)

gmx-mdmat - Calculate residue contact maps

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>]


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 files:

Trajectory: xtc trr cpt gro g96 pdb tng
Structure+mass(db): tpr gro g96 pdb brk ent
Index file

Options to specify output files:

X PixMap compatible matrix file
X PixMap compatible matrix file
xvgr/xmgr file

Other options:

Time of first frame to read from trajectory (default unit ps)
Time of last frame to read from trajectory (default unit ps)
Only use frame when t MOD dt = first time (default unit ps)
xvg plot formatting: xmgrace, xmgr, none
trunc distance
Discretize distance in this number of levels

gmx(1)

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2023, GROMACS development team

February 3, 2023 2022.5