g_mdmat (1) - Linux Manuals

g_mdmat: calculates residue contact maps


g_mdmat - calculates residue contact maps



g_mdmat -f traj.xtc -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -t real -nlevels int


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.


-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 


 Print help 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)

 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-t real 1.5
 trunc distance

-nlevels int 40
 Discretize distance in  levels



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