Man page - gmx-mdmat(1)
Packages contains this manual
- gmx-trjorder(1)
- gmx-wheel(1)
- gmx-genion(1)
- gmx-energy(1)
- gmx-rmsdist(1)
- gmx-sham(1)
- gmx-helixorient(1)
- gmx-select(1)
- gmx-nmeig(1)
- gmx-density(1)
- gmx-genrestr(1)
- gmx-bar(1)
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- gmx-filter(1)
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- gmx_d(1)
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- gmx-hydorder(1)
- gmx-editconf(1)
- gmx-msd(1)
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- gmx-cluster(1)
- gmx-saltbr(1)
- gmx-potential(1)
- gmx-current(1)
- gmx-freevolume(1)
- gmx-make_ndx(1)
- gmx-enemat(1)
- gmx(1)
- gmx-gyrate(1)
- gmx-solvate(1)
- gmx-densmap(1)
- gmx-rotacf(1)
- gmx-helix(1)
- gmx_mpi(1)
- gmx-convert-tpr(1)
- gmx-convert-trj(1)
- gmx-polystat(1)
- gmx-angle(1)
- gmx-xpm2ps(1)
- gmx-pdb2gmx(1)
- gmx-sasa(1)
- gmx-x2top(1)
- gmx-trjcat(1)
- gmx-h2order(1)
- gmx-nmr(1)
- gmx-dump(1)
- gmx-spol(1)
- gmx-distance(1)
- gmx-clustsize(1)
- gmx-rama(1)
- gmx-chi(1)
- gmx-pme_error(1)
- gmx-order(1)
- gmx-gangle(1)
- gmx-eneconv(1)
- gmx-tune_pme(1)
- gmx-grompp(1)
- gmx-make_edi(1)
- gmx-trajectory(1)
- gmx-dipoles(1)
- gmx-awh(1)
- gmx-nonbonded-benchmark(1)
- gmx-analyze(1)
- demux(1)
- gmx-disre(1)
- gmx-saxs-legacy(1)
- gmx-sigeps(1)
- gmx-mdmat(1)
- xplor2gmx(1)
- gmx-check(1)
- gmx-vanhove(1)
- gmx-dssp(1)
- gmx-densorder(1)
- gmx-principal(1)
- gmx-mindist(1)
- gmx-spatial(1)
- gmx-wham(1)
- gmx-rmsf(1)
- gmx-dos(1)
- gmx-mk_angndx(1)
- gmx-nmens(1)
- gmx-dielectric(1)
- gmx-sorient(1)
- gmx-help(1)
- gmx-hbond-legacy(1)
- gmx-sans-legacy(1)
- gmx-gyrate-legacy(1)
- gmx-hbond(1)
- gmx-rotmat(1)
- gmx-extract-cluster(1)
- gmx-rms(1)
- gmx-dyecoupl(1)
- gmx-rdf(1)
- gmx-pairdist(1)
- gmx-trjconv(1)
- gmx-traj(1)
- gmx_mpi_d(1)
- gmx-report-methods(1)
- gmx-nmtraj(1)
apt-get install gromacs-data
Manual
GMX-MDMAT
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
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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2025, GROMACS development team