OK, so let me ask you this last question (by the way, I've already checked
the manual and several references therein, but I cannot get a clear answer
to my following question):
If some system consists of a molecule A and water, would you say that it's
possible to do an integration A-WAT (or A-environment as it's usually
called), so that
initial state: A+WAT, interactions: A-A, WAT-WAT, A-WAT
final state: WAT with interactions WAT-WAT,
A with interaction A-A (i. e., including eel and VDW)?
Or may be the final state is the above but without eel and VDW in the A-A
interactions?
Thanks,
Ignacio
On Thu, Mar 17, 2011 at 11:06 AM, <steinbrt.rci.rutgers.edu> wrote:
> Hi,
>
> > Thanks for your answer. So, in the charge part of TI all interactions are
> > reduced. But I don't understand what you say about the SC interactions. I
>
> the charges themselves are reduced, not the charge-charge interactions
> (This makes a difference in e.g. ion solution structures).
>
> > assume in the VDW part of TI you also tell amber to put all the VDW
> > parameters (corresponding to A) to zero, so that even internal
> > interactions
> > (A-A) are reduced. Is this correct?
>
> its more complicated than this. What you describe is the dummy atom
> approach, which is not suggested anymore in Amber. Chapter 4 of the Amber
> manual has a lot more info and citations on this.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Thu Mar 17 2011 - 08:30:05 PDT
