Query: g_mdmat
OS: debian
Section: 1
Format: Original Unix Latex Style Formatted with HTML and a Horizontal Scroll Bar
g_mdmat(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_mdmat(1)NAMEg_mdmat - calculates residue contact maps VERSION 4.5.4-dev-20110404-bc5695cSYNOPSISg_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 intDESCRIPTIONg_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 fileOTHER 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 levelsSEE ALSOgromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_mdmat(1)
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