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g_mdmat_d
Langue: en
Version: 259731 (debian - 07/07/09)
Section: 1 (Commandes utilisateur)
NAME
g_mdmat - calculates residue contact mapsSYNOPSIS
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 intDESCRIPTION
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.FILES
-f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-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]h noPrint 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)
-[no]xvgr yes
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
SEE ALSO
gromacs(7)More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre