Matt Wyczalkowski wrote:
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?
Having two ways allows for more flexibility. Some force fields might be
prescriptive about charges for certain atom types, some might not be.
Accordingly, [atoms] 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?
I don't know, but I expect [atoms].
Mark
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