ngmx(1) - Linux man page

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