gmx view¶
Synopsis¶
gmx view [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-n [<.ndx>]] [-b <time>] [-e <time>] [-dt <time>]
Description¶
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¶
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)- Index file
Other options:
-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)
Known Issues¶
- Balls option does not work
- Some times dumps core without a good reason