[gmx-users] Negative number of RMSD calculations left in g_cluster

Bob Johnson bobjohnson1981 at gmail.com
Fri Mar 26 22:52:19 CET 2010

Hello everyone,
I am attempting to use g_cluster on a large data set (about 69000)
frames. I'm on a machine that has 48 GB of RAM, so I shouldn't be
running out of memory. As g_cluster runs, it counts down the number of
RMSD calculations left. Normally this number is positive (as it should
be). Instead of stopping at 0, however, the calculation keeps on going
and displays a negative number of RMSD calculations that remain. This
negative keeps on getting more and more negative until eventually the
machine runs out of memory and I get a seg fault.

I have run this same exact calculation skip 2 (35000 frames instead of
69000) and it works fine. What is the reason for the negative number
of RMSD calculations and how can it be fixed?

Bob Johnson, PhD
Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122

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