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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