g_rms gives nonsense values when the number of atoms differs between tpr and xtc
If the number of atoms in tpr is less than xtc, g_rms will generate larger RMS values than correct. Some initialization problem in the xp array is to blame I think.
#2 Updated by David van der Spoel about 10 years ago
The specific case was a protein complex where I wanted to do an RMSD of the protein in the complex with respect to a pdb/tpr file. At the minimum, g_rms should not generate incorrect values but it would be better to be able to compare trajectories to different other files (e.g. when comparing to homologues).