On Mon, Dec 10, 2012, Yulin Huang wrote:
> For states V0 and V1 unperturbed atoms (in other words, the same atoms
> with the same coordinates), do they need to have exactly the same charges?
> It seems that for V0 ->V1, V1 may copy the charges from V0 and for V1->V0,
> V0 may copy the charges from V1. This may lead to the wrong Hamiltonian.
I think there is a nomenclature problem here: TI has no conception of
what is a "perturbed" or an "unperturbed" atom. It simply computes the
energy difference between the V0 and the V1 states of the entire system.
I'd think of an atom that is changing its charge as being "perturbed", but the
program doesn't keep any such list.
I'd be curious to know what it is that makes you think that "V1 may copy the
charges from V0". As far as I can see, nothing like this takes place.
Note also that with softcore, there *is* a distinction between
"appearing/disappearing" atoms (which exist in one prmtop file but no the
other) and common atoms (which exist in both prmtop files). Common atoms
don't need to have the same charges in the two endpoints.
[Aside: "appearing/disappearing" is actually a bad choice of wording; such
atoms are decoupled from their surroundings during the TI process--they don't
actually disappear.]
...dac
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Received on Mon Dec 10 2012 - 12:00:02 PST
