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 - 08:30:04 PDT
