[gmx-users] g_covar & g_anaeig problems

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Mar 26 08:54:47 CET 2010

Hi Jared,

Can you post the exact series of commands you used to come to this
point, including the selections you used and what constitutes these
selections if they are not standard? Please also indicate what was in
the trajectory you started off with (xtc-grps).



On Thu, Mar 25, 2010 at 10:31 PM, Jared James Thompson
<thompsjj at purdue.edu> wrote:
> Greetings,
> I'm trying to use g_covar to generate a covariance matrix, followed by g_anaeig
> to analyze the data. The trajectory is a list of clusters generated by g_cluster
> in .trr format. gmxcheck seems to think that the input trajectory is fine but
> the cluster trajectory gives this error when gmxcheck is used:
> Timesteps at t=9974 don't match (2, 4)
> Timesteps at t=9978 don't match (4, 2)
> for every t += 4.
> g_covar crashes when I use my trajectory, giving the message:
> WARNING: number of atoms in tpx (730) and trajectory (730) do not match
> and then usually gives a segmentation fault message or a memory error.
> Help?
> best,
> Jared
> --
> Jared James Thompson
> Department of Medicinal Chemistry and Molecular Pharmacology
> Laboratory for Computational Drug Design and Biology
> RHPH 504C
> Heine Pharmacy Building
> 575 Stadium Mall Drive
> West Lafayette, IN  47907-2091
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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