GROMACS version: 2018.1
GROMACS modification: No
It might look silly to ask, but I was just curious about the hierarchy of data read in GROMACS. I just noticed something when a topology file is read and I wanted to ask what the reason is.
[ atomtypes ] section of the topology file, one can specify the masses and charges in the 3rd and 4th columns, as indicated here. However, I noticed that both masses and charges are read from the
[ atoms ] section of the topology and not the
[ atomtypes ]. Meaning that even if the masses and charges are set to zero in the
[ atomtypes ] section, both can be updated later in the
[ atoms ] section.
Then here is the question: if masses and charges in the
[ atoms ] section is prioritized over the
[ atomtypes ] section, why is there a need to have them also mentioned in the
[ atomtypes ]? I can understand this for the charges of course, but why masses? Are they expected to change?
I hope I could make what I mean clear, and sorry if it seems stupid.