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)-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