g_mdmat(1)
NAME
g_mdmat - calculates residue contact maps
SYNOPSIS
g_mdmat -f traj.xtc -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -t real -nlevels int
DESCRIPTION
g_mdmat makes distance matrices consisting of the smallest distance
between residue pairs. With -frames these distance matrices can be
stored as a function of time, to be able to see differences in tertiary
structure as a funcion of time. If you choose your options unwise, this
may generate a large output file. 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 xpm2ps to make a PostScript
(tm) plot.
FILES
- -f traj.xtc Input
- Generic trajectory: xtc trr trj gro g96 pdb
- -s topol.tpr Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
- -n index.ndx Input, Opt.
- Index file
- -mean dm.xpm Output
- X PixMap compatible matrix file
- -frames dmf.xpm Output, Opt.
- X PixMap compatible matrix file
- -no num.xvg Output, Opt.
- xvgr/xmgr file
OTHER OPTIONS
- -[no]h no
- Print help info and quit
- -nice int 19
- Set the nicelevel
- -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)
- -[no]xvgr yes
- Add specific codes (legends etc.) in the output xvg files for the
- xmgrace program
- -t real 1.5
- trunc distance
- -nlevels int 40
- Discretize distance in levels
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.