.TH g_mdmat 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_mdmat - calculates residue contact maps

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-mean" " dm.xpm "
.BI "\-frames" " dmf.xpm "
.BI "\-no" " num.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-xvg" " enum "
.BI "\-t" " real "
.BI "\-nlevels" " int "
.SH DESCRIPTION
\&\fB g_mdmat\fR makes distance matrices consisting of the smallest distance
\&between residue pairs. With \fB \-frames\fR, 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 \fB xpm2ps\fR to make a PostScript (tm) plot.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-mean" " dm.xpm" 
.B Output
 X PixMap compatible matrix file 

.BI "\-frames" " dmf.xpm" 
.B Output, Opt.
 X PixMap compatible matrix file 

.BI "\-no" " num.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-t"  " real" " 1.5   " 
 trunc distance

.BI "\-nlevels"  " int" " 40" 
 Discretize distance in  levels

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.