gmx-view(1) GROMACS Manual gmx-view(1)NAMEgmx-view - View a trajectory on an X-Windows terminal
SYNOPSIS
gmx view [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]] [-n [<.ndx>]]
[-nice <int>] [-b <time>] [-e <time>] [-dt <time>]
DESCRIPTION
gmx view is the GROMACS trajectory viewer. This program reads a trajec‐
tory 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, trans‐
lation 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 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
- Balls option does not work
- Some times dumps core without a good reason
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-view(1)
