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| GMX-MDMAT(1) | GROMACS | GMX-MDMAT(1) |
NAME
gmx-mdmat - Calculate residue contact maps
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
SEE ALSO
gmx(1)
More information about GROMACS is available at <http://www.gromacs.org/>.
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| February 10, 2025 | 2025.0 |
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