g_saltbr(1) [debian man page]

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

NAME

       g_saltbr - computes salt bridges

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_saltbr -f traj.xtc -s topol.tpr -[no]h -[no]version -nice int -b time -e time -dt time -t real -[no]sep

DESCRIPTION

	g_saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways.  A
       minimum distance can be given (i.e. a cut-off), such that groups that are never closer than that distance will not be plotted.

       Output will be in a number of fixed filenames,  min-min.xvg,  plus-min.xvg and  plus-plus.xvg, or files for every individual  ion  pair	if
       the  -sep option is selected. In this case, files are named as  sb-(Resname)(Resnr)-(Atomnr).  There may be  many such files.

FILES

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

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

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)

       -t real 1000
	trunc distance

       -[no]sepno
	Use separate files for each interaction (may be MANY)

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						       g_saltbr(1)

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)