[gmx-users] problem with using VMD to view the trajectory

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jul 19 14:22:17 CEST 2008

Hi Hui Sun,

Did you verify the integrity of the trajectory with gmxcheck? If not,
you should and if you find that the trajectory is not good, show us
what's wrong. If the trajectory is not garbled, but is interpreted
wrongly by VMD, try the VMD user list.


2008/7/19 hui sun <sunhui1018 at yahoo.com.cn>:
> Dear all,
> I am a new user of gromacs. Recently, I have installed the gromacs-3.3.3
> software package on my computer. After installation was complete, I run the
> example of water in the online reference manual. The trajectory file is OK
> for the first time. But when I run it for the second time, and used vmd to
> look at the trajectory, I found that the trajetory is disordered, the frames
> in the VMD main are equal to 2, and the output file .gro seems ok. What's
> worry with my gromacs? I don't know what to do now and how can I overcome
> this. Could you help me?
> Thanks in advance!
> Hui Sun
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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