Hi, Prof David Case,
Thank you so much for your reply. I am running a test now. I do not
see how the charges transit from V0 to V1 with different lamdas. Thus I
think "V1 may copy the charges from V0".
I just ran into this discussion during a committee meeting.
Yulin
On Mon, Dec 10, 2012 at 2:45 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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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--
Yulin "Joyce" Huang
Ph.D Candidate
Computational Chemistry (CADD)
Advisor: Dr. Robert C. Rizzo
State University of New York at Stony Brook
Stony Brook NY,11790
Office: (631)632-8519
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Received on Mon Dec 10 2012 - 12:00:03 PST
