[gmx-users] g_cluster stopped - malloc failed

[Justin Lemkul]

On 3/27/13 5:40 AM, Zalikha Ibrahim wrote:
> Good day to all GMX users,
>
> I have two trajectories, 0-10ns and 10-20ns. I merged both .trr file using
> trjcat with option -overwrite.
>
>> trjcat -f npt.trr npt2.trr -o npt_cat.trr -overwrite
>
> Converted into .xtc and then I tried using the g_cluster tool in order to
> cluster the trajectories.
>
>> g_cluster -f npt_cat.xtc -s npt.gro -method gromos -cl cluster.pdb -g
> cluster.log -cutoff 0.15 -b 4000
>
> I choose c-alpha for rmsd calculation
> I choose protein for output
> It appeared this following line at frame 5000.
> ..
> Reading frame    5000 time 14000.000   malloc failed
>
> I would be grateful if someone can tell me why it failed? And why does the
> time didnt appeared as it should? (e.g. reading frame 5000 time 10000.00,
> as it is written at every 2ps).
>

The frame and time values are only updated periodically in the screen output. 
What you've posted above does not indicate that frame 5000 corresponds to the 
time at 14000 ps, just that g_cluster was busy processing and hadn't yet updated 
the printed output.  The "malloc failed" error means you have run out of memory. 
  Either reduce the number of frames or reduce the size of the problem. 
g_cluster requires a lot of memory.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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