GROMACS version: 2021
GROMACS modification: Yes
this is more of a ‘philosophical’ question rather than a technical one: why does
gmx grompp issue a warning if the number of atoms in the
-r restraints file does not match the number of atoms in the
-p topology file, rather than just a note?
My understanding is that it makes perfectly sense to have only the atoms that are effectively restrained in the restraints file, and I guess I am not the only only one doing it; is the warning issued just because this is not ‘as intended’ and GROMACS fears the user is doing something wrong, or is there some deeper reason (i.e. for some reason it’s more efficient to have topology and restraints exacty matching)?