NAME¶

g_mdmat - calculates residue contact maps VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS¶

g_mdmat -f traj.xtc -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h -[no]version -nice int -b time -e time -dt time -xvg enum -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 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 xpm2ps to make a PostScript (tm) plot.

FILES¶

-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb -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]hno
Print help info and quit -[no]versionno
Print version 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) -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -t real 1.5
trunc distance -nlevels int 40
Discretize distance in levels

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.