Hi, Thomas. Thank you so much for your detailed explanation.
Yulin
On Mon, Dec 10, 2012 at 2:26 PM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > 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?
>
> no, they can but don't have to. This means implicitly that if they do not
> have the same charge, your transformation free energy accounts for
> changing this charge, plus whatever else is changing in the unique atoms.
> The common atom electrostatics is scaled linearly, but that is normally
> not a reason for concern.
>
> So you need to make sure to compute free energy changes in which the
> overall charge changes cancel out, since they do not contribute meaningful
> total energy terms.
>
> Doing the same transformation (e.g. between two ligands with differing
> charges) in two environments (e.g. in two different solvents) yields
> cancelling internal electrostatics terms and meaningful delta-delta-Gs
>
> So typically, having different charges on common atoms is something that
> will occur in your simulations, that will influence dVdl and that is fine
> :-)
>
> Thomas
>
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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 - 11:30:04 PST
