ngmx(1) [debian man page]

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

NAME

       ngmx - displays a trajectory

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       ngmx -f traj.xtc -s topol.tpr -n index.ndx -[no]h -[no]version -nice int -b time -e time -dt time

DESCRIPTION

	 ngmx  is the GROMACS trajectory viewer. This program reads a trajectory file, a run input file and an index file and plots a 3D structure
       of your molecule on your standard X Window screen. No need for a high end graphics workstation, it even works on Monochrome screens.

       The following features have been implemented: 3D view, rotation, translation and scaling of your molecule(s), labels on atoms, animation of
       trajectories, hardcopy in PostScript format, user defined atom-filters runs on MIT-X (real X), open windows and motif, user friendly menus,
       option to remove periodicity, option to show computational box.

       Some of the more common X command line options can be used:  -bg,  -fg change colors,  -font fontname changes the font.

FILES

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

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

       -n index.ndx Input, Opt.
	Index file

OTHER OPTIONS

       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 0
	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)

KNOWN PROBLEMS

       - Balls option does not work

       - Some times dumps core without a good reason

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011							   ngmx(1)

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

NAME

       g_filter - frequency filters trajectories, useful for making smooth movies

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS

       g_filter  -f  traj.xtc  -s  topol.tpr  -n index.ndx -ol lowpass.xtc -oh highpass.xtc -[no]h -[no]version -nice int -b time -e time -dt time
       -[no]w -nf int -[no]all -[no]nojump -[no]fit

DESCRIPTION

	g_filter performs frequency filtering on a trajectory.	The filter shape is cos(pi t/A) + 1 from -A to +A, where A is given by the  option
       -nf  times  the	time step in the input trajectory.  This filter reduces fluctuations with period A by 85%, with period 2*A by 50% and with
       period 3*A by 17% for low-pass filtering.  Both a low-pass and high-pass filtered trajectory can be written.

       Option  -ol writes a low-pass filtered trajectory.  A frame is written every  -nf input frames.	This ratio of  filter  length  and  output
       interval  ensures a good suppression of aliasing of high-frequency motion, which is useful for making smooth movies. Also averages of prop-
       erties which are linear in the coordinates are preserved, since all input frames are weighted equally in the output.  When all  frames  are
       needed, use the	-all option.

       Option	-oh  writes  a	high-pass filtered trajectory.	The high-pass filtered coordinates are added to the coordinates from the structure
       file. When using high-pass filtering use  -fit or make sure you use a trajectory that has been fitted on the coordinates in  the  structure
       file.

FILES

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

       -s topol.tpr Input, Opt.
	Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
	Index file

       -ol lowpass.xtc Output, Opt.
	Trajectory: xtc trr trj gro g96 pdb

       -oh highpass.xtc Output, Opt.
	Trajectory: xtc trr trj gro g96 pdb

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

       -nf int 10
	Sets the filter length as well as the output interval for low-pass filtering

       -[no]allno
	Write all low-pass filtered frames

       -[no]nojumpyes
	Remove jumps of atoms across the box

       -[no]fitno
	Fit all frames to a reference structure

SEE ALSO

       gromacs(7)

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

								  Mon 4 Apr 2011						       g_filter(1)