gmx-view1
View a trajectory on an x-windows terminal
Usage
gmx view [-f[<.xtc/.trr/...>]] [-s[<.tpr>]] [-n[<.ndx>]] [-b<time>][-e<time>] [-dt<time>]
Overview
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)
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Trajectory: xtc trr cpt gro g96 pdb tng |
|---|---|
-s [<.tpr>] (topol.tpr)
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Portable xdr run input file |
-n [<.ndx>] (index.ndx) (Optional)
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Index file |
Other options:
-b <time> (0)
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Time of first frame to read from trajectory (default unit ps) |
|---|---|
-e <time> (0)
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Time of last frame to read from trajectory (default unit ps) |
-dt <time> (0)
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Only use frame when t MOD dt = first time (default unit ps) |
Known issues
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Balls option does not work |
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•
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Some times dumps core without a good reason |
Releases
5 releases since Debian 8 (Jessie); the text changed 4 times.