[gmx-users] RMSD Calculation

[Bob Johnson]

Hello everyone,
I'm trying to calculate the rmsd of a single stranded DNA adsorbed to a carbon
nanotube. I'm getting the following error when I use g_rms:
Reading frame       0 time    0.000   There were 312 inconsistent shifts. Check
your topology

I'm comparing only the ssDNA to it's reference structure - water or the nanotube
should not factor into the calculation. The nanotube atoms remain restrained
throughout the trajectory. I get that message many, many times while Gromacs
calculates the rmsd. What does it mean?

Also, to my understanding, the rmsd neglects center of mass translational or
rotational motion of a molecule. Thus, only relative changes in the atomic
positions of a molecule will factor into the rmsd. Is that correct?
Thanks,
Bob Johnson