[gmx-users] Defining charges: [atomtypes] vs [atoms]

[Matt Wyczalkowski]

Looking through the documentation, it seems like the charge of an atom
may be defined in one of two ways: in the [atomtypes] directive, or in
the [atoms] directive.  In the past, I've always made them identical,
but I have seen examples where they differ.

Why are there two ways to define an atom's charge, and which
definition takes precedence?  Also, during a free energy calculation
where an atom mutates typeA -> typeB, are the charge values as defined
in the [atomtypes] section or [atoms] section used?

Thanks --

Matt