g_rms uses incorrect masses when reference is a PDB/GRO file
g_rms uses a massweighted cRMS by default (which isn't documented).
When the reference state is a TPR file the masses are set correctly, but when
using a PDB or GRO file they are guessed incorrectly - probably from the atom names.
IMHO, the proper action would be to not use massweighting unless we are certain masses are correct.
#1 Updated by Berk Hess about 14 years ago
g_rms should have a (documented) -mw option, like g_confrms,
which is turned on by default.
The mass guessing is a more general issue.
There is an atommass.dat library file which is used to guess
the masses from the names. For proteins this works pretty
well, but it can produce some incorrect masses for any other type of system.
So we should decide if should get rid of the atommass.dat altogether,
or use it everywhere, also for g_rms.