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gmx-view - Online in the Cloud

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This is the command gmx-view that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-view - View a trajectory on an X-Windows terminal

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)
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

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