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
More information about GROMACS is available at <- http://www.gromacs.org/>.
COPYRIGHT
2020, GROMACS development team