gmx view [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]] [-b <time>] [-e <time>] [-dt <time>]
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 files:
- -f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
- -s [<.tpr>] (topol.tpr)
Portable xdr run input file
- -n [<.ndx>] (index.ndx) (Optional)
- -b <time> (0)
Time of first frame to read from trajectory (default unit ps)
- -e <time> (0)
Time of last frame to read from trajectory (default unit ps)
- -dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
- Balls option does not work
- Some times dumps core without a good reason
More information about GROMACS is available at <http://www.gromacs.org/>.
2020, GROMACS development team