[gmx-users] g_cluster stopped - malloc failed

[Zalikha Ibrahim]

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).

Thanks in advance. Appreciate your help.

Zalikha Ibrahim