[gmx-users] Inconsistent shifts in g_rms

Bob Johnson robertjo at physics.upenn.edu
Sat Feb 18 01:16:04 CET 2006

Hello everyone,
My system consists of an infinite carbon nanotube, water, and single stranded
Whenever I run g_rms to calculate the rms displacement of the DNA or nanotube I
get the following error message over and over again:

There were 36 inconsistent shifts. Check your topology

It is always 36 no matter which group I pick as a reference structure. The
program still calculates a reasonable looking rmsd function. However, I still
wonder what this error message means and why I'm getting it. Any ideas?
Bob Johnson

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