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

6       gmx-mdmat - Calculate residue contact maps
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SYNOPSIS

9          gmx mdmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
10                    [-mean [<.xpm>]] [-frames [<.xpm>]] [-no [<.xvg>]]
11                    [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
12                    [-t <real>] [-nlevels <int>]
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DESCRIPTION

15       gmx  mdmat  makes distance matrices consisting of the smallest distance
16       between residue pairs. With -frames, these  distance  matrices  can  be
17       stored  in order to see differences in tertiary structure as a function
18       of time. If you choose your options unwisely, this may generate a large
19       output file. By default, only an averaged matrix over the whole trajec‐
20       tory is output.  Also a count of the number of  different  atomic  con‐
21       tacts between residues over the whole trajectory can be made.  The out‐
22       put can be processed with gmx xpm2ps to make a PostScript (tm) plot.
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OPTIONS

25       Options to specify input files:
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27       -f [<.xtc/.trr/...>] (traj.xtc)
28              Trajectory: xtc trr cpt gro g96 pdb tng
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30       -s [<.tpr/.gro/...>] (topol.tpr)
31              Structure+mass(db): tpr gro g96 pdb brk ent
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33       -n [<.ndx>] (index.ndx) (Optional)
34              Index file
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36       Options to specify output files:
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38       -mean [<.xpm>] (dm.xpm)
39              X PixMap compatible matrix file
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41       -frames [<.xpm>] (dmf.xpm) (Optional)
42              X PixMap compatible matrix file
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44       -no [<.xvg>] (num.xvg) (Optional)
45              xvgr/xmgr file
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47       Other options:
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49       -b <time> (0)
50              Time of first frame to read from trajectory (default unit ps)
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52       -e <time> (0)
53              Time of last frame to read from trajectory (default unit ps)
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55       -dt <time> (0)
56              Only use frame when t MOD dt = first time (default unit ps)
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58       -xvg <enum> (xmgrace)
59              xvg plot formatting: xmgrace, xmgr, none
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61       -t <real> (1.5)
62              trunc distance
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64       -nlevels <int> (40)
65              Discretize distance in this number of levels
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SEE ALSO

68       gmx(1)
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70       More    information    about    GROMACS    is    available    at     <‐
71       http://www.gromacs.org/>.
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74       2022, GROMACS development team
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792022.3                           Sep 02, 2022                     GMX-MDMAT(1)
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