g_ngmx (1) Linux Manual Page

ngmx – displays a trajectory

VERSION 4.0.1

Synopsis

ngmx -f traj.xtc -s topol.tpr -n index.ndx -[no]h -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

-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/>.