Man page - gmx-mdmat(1)
Packages contas this manual
- gmx-wham(1)
- gmx-trjcat(1)
- gmx-confrms(1)
- gmx_d(1)
- gmx-xpm2ps(1)
- gmx-make_edi(1)
- gmx-solvate(1)
- gmx-awh(1)
- gmx-help(1)
- gmx-hydorder(1)
- gmx-velacc(1)
- gmx-order(1)
- gmx-clustsize(1)
- gmx-densorder(1)
- gmx-msd(1)
- gmx-saxs-legacy(1)
- gmx-covar(1)
- gmx-tcaf(1)
- gmx-filter(1)
- gmx-rms(1)
- gmx-bundle(1)
- gmx-vanhove(1)
- gmx-enemat(1)
- gmx-rama(1)
- gmx-spatial(1)
- gmx-nmens(1)
- gmx-mdmat(1)
- gmx-rotmat(1)
- gmx(1)
- gmx-eneconv(1)
- gmx-h2order(1)
- gmx-current(1)
- gmx-genion(1)
- gmx-rmsdist(1)
- gmx-report-methods(1)
- gmx-distance(1)
- gmx-insert-molecules(1)
- demux(1)
- gmx-dielectric(1)
- gmx-sans-legacy(1)
- gmx-sigeps(1)
- gmx-genrestr(1)
- gmx-analyze(1)
- gmx-convert-tpr(1)
- gmx-potential(1)
- gmx-wheel(1)
- gmx-mk_angndx(1)
- gmx-x2top(1)
- gmx-genconf(1)
- gmx-mindist(1)
- gmx-dipoles(1)
- gmx-polystat(1)
- gmx-hbond-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-make_ndx(1)
- gmx-nonbonded-benchmark(1)
- gmx-sham(1)
- gmx-nmr(1)
- xplor2gmx(1)
- gmx-densmap(1)
- gmx-bar(1)
- gmx-trajectory(1)
- gmx-sasa(1)
- gmx-dos(1)
- gmx-principal(1)
- gmx-pme_error(1)
- gmx-hbond(1)
- gmx-dump(1)
- gmx-traj(1)
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- gmx-trjconv(1)
- gmx_mpi(1)
- gmx-density(1)
- gmx-pdb2gmx(1)
- gmx-spol(1)
- gmx-cluster(1)
- gmx-select(1)
- gmx-rmsf(1)
- gmx-angle(1)
- gmx-saltbr(1)
- gmx-scattering(1)
- gmx-energy(1)
- gmx-dyecoupl(1)
- gmx-disre(1)
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- gmx-nmtraj(1)
- gmx-helix(1)
- gmx-trjorder(1)
- gmx-grompp(1)
- gmx-gangle(1)
- gmx-dssp(1)
- gmx-convert-trj(1)
- gmx-sorient(1)
- gmx-chi(1)
- gmx-anaeig(1)
- gmx-lie(1)
- gmx-helixorient(1)
- gmx-mdrun(1)
- gmx-editconf(1)
- gmx-rdf(1)
- gmx_mpi_d(1)
- gmx-rotacf(1)
- gmx-nmeig(1)
- gmx-gyrate(1)
apt-get install gromacs-data
Manual
| 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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| May 12, 2025 | 2025.2 |