g_mdmat(1) - Linux man page

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