g_mdmat

Section: GROMACS suite, VERSION 4.5 (1) Updated: Thu 26 Aug 2010 Local index Up

NAME

g_mdmat - calculates residue contact maps

VERSION 4.5

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 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
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

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Time: 21:13:23 GMT, April 16, 2011