gmx view

Main Table of Contents VERSION 5.0


gmx view [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
         [-nice ] [-b 


gmx view 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.


Options to specify input and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
Other options:

-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 Issues