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This is the command gmx-mdmat that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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)
First frame (ps) to read from trajectory

-e <time> (0)
Last frame (ps) to read from trajectory

-dt <time> (0)
Only use frame when t MOD dt = first time (ps)

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-t <real> (1.5)
trunc distance

-nlevels <int> (40)
Discretize distance in this number of levels

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