[gmx-users] Error message in g_rms

[Bob Johnson]

Hello everyone,
I am studying the adsorption of single stranded DNA on a carbon nanotube. I
would like to obtain an rms displacement fit of the DNA to its initial
conformation. Thus, I've been using the flag -fit rot+trans when I run g_rms. I
get the following stream of error messages:

Reading frame      40 time   30.000   There were 36 inconsistent shifts. Check
your topology

I get it over and over again. In the end it does generate a reasonable looking
rmsd.xvg file. Does anyone know what causes this message?
Thanks,
Bob Johnson