1g_mdmat(1)                GROMACS suite, VERSION 4.5                g_mdmat(1)
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NAME

6       g_mdmat - calculates residue contact maps
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8       VERSION 4.5
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SYNOPSIS

11       g_mdmat  -f  traj.xtc  -s  topol.tpr  -n index.ndx -mean dm.xpm -frames
12       dmf.xpm -no num.xvg -[no]h -[no]version -nice int -b time -e  time  -dt
13       time -xvg enum -t real -nlevels int
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DESCRIPTION

16       g_mdmat  makes  distance  matrices  consisting of the smallest distance
17       between residue pairs. With -frames  these  distance  matrices  can  be
18       stored as a function of time, to be able to see differences in tertiary
19       structure as a funcion of time. If you choose your options unwise, this
20       may  generate a large output file. Default only an averaged matrix over
21       the whole trajectory is output.  Also a count of the number of  differ‐
22       ent  atomic  contacts between residues over the whole trajectory can be
23       made.  The output can be processed with xpm2ps  to  make  a  PostScript
24       (tm) plot.
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FILES

27       -f traj.xtc Input
28        Trajectory: xtc trr trj gro g96 pdb cpt
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30       -s topol.tpr Input
31        Structure+mass(db): tpr tpb tpa gro g96 pdb
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33       -n index.ndx Input, Opt.
34        Index file
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36       -mean dm.xpm Output
37        X PixMap compatible matrix file
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39       -frames dmf.xpm Output, Opt.
40        X PixMap compatible matrix file
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42       -no num.xvg Output, Opt.
43        xvgr/xmgr file
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OTHER OPTIONS

47       -[no]hno
48        Print help info and quit
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50       -[no]versionno
51        Print version info and quit
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53       -nice int 19
54        Set the nicelevel
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56       -b time 0
57        First frame (ps) to read from trajectory
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59       -e time 0
60        Last frame (ps) to read from trajectory
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62       -dt time 0
63        Only use frame when t MOD dt = first time (ps)
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65       -xvg enum xmgrace
66        xvg plot formatting:  xmgrace,  xmgr or  none
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68       -t real 1.5
69        trunc distance
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71       -nlevels int 40
72        Discretize distance in  levels
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SEE ALSO

76       gromacs(7)
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78       More   information  about  GROMACS  is  available  at  <http://www.gro‐
79       macs.org/>.
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83                                Thu 26 Aug 2010                     g_mdmat(1)
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