g_mdmat(1) [debian man page]

g_mdmat(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_mdmat(1)

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

       -nlevels int 40
	Discretize distance in	levels

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							g_mdmat(1)

g_disre(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_disre(1)

NAME

       g_disre - analyzes distance restraints

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_disre	-s  topol.tpr  -f  traj.xtc  -ds  drsum.xvg  -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q
       viol.pdb -c clust.ndx -x matrix.xpm -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ntop int -maxdr real  -nlevels
       int -[no]third

DESCRIPTION

	 g_disre  computes violations of distance restraints.  If necessary, all protons can be added to a protein molecule using the  g_protonate
       program.

       The program always computes the instantaneous violations rather than time-averaged, because this analysis is done from  a  trajectory  file
       afterwards it does not make sense to use time averaging. However, the time averaged values per restraint are given in the log file.

       An index file may be used to select specific restraints for printing.

       When the optional  -q flag is given a  .pdb file coloured by the amount of average violations.

       When the  -c option is given, an index file will be read containing the frames in your trajectory corresponding to the clusters (defined in
       another manner) that you want to analyze. For these clusters the program will compute average violations using the  third  power  averaging
       algorithm and print them in the log file.

FILES

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -f traj.xtc Input
	Trajectory: xtc trr trj gro g96 pdb cpt

       -ds drsum.xvg Output
	xvgr/xmgr file

       -da draver.xvg Output
	xvgr/xmgr file

       -dn drnum.xvg Output
	xvgr/xmgr file

       -dm drmax.xvg Output
	xvgr/xmgr file

       -dr restr.xvg Output
	xvgr/xmgr file

       -l disres.log Output
	Log file

       -n viol.ndx Input, Opt.
	Index file

       -q viol.pdb Output, Opt.
	Protein data bank file

       -c clust.ndx Input, Opt.
	Index file

       -x matrix.xpm Output, Opt.
	X PixMap compatible matrix 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)

       -[no]wno
	View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -ntop int 0
	Number of large violations that are stored in the log file every step

       -maxdr real 0
	Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.

       -nlevels int 20
	Number of levels in the matrix output

       -[no]thirdyes
	Use inverse third power averaging or linear for matrix output

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							g_disre(1)