g_mdmat

Main Table of Contents

VERSION 4.6.3
Fri 5 Jul 2013


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

optionfilenametypedescription
-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

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no 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 this number of levels


http://www.gromacs.org
gromacs@gromacs.org