On Tue, Nov 19, 2013 at 7:45 PM, kurisaki <
kurisaki.ncube.human.nagoya-u.ac.jp> wrote:
>
> Both simulations were performed with the same input file shown below,
> But differ in presence or absence of explicit water molecules.
>
> > You have igb=1 set. This is continuum solvent.
> Yes, I use igb=1 because I found igb=0 does not work with idecomp in
> Amber12.
> But I set gbsa=0 to give zero value for GB-terms and in fact
> they are zero (see right two columns).
> Furthermore, internal, electrostatic, and vdW terms does not include
> GB terms, doesn't they?
>
> I do not think that GB affects such energy terms...
>
Carlos is right. There have been numerous discussions on this list
describing (in varying detail) why the GB energy is not pairwise
decomposable. It would be worth searching back through these posts to
convince yourself that this is true. Doing a google search of "GB not
pairwise decomposable" yields many results.
One of which is this: http://archive.ambermd.org/201309/0154.html, which I
think offers a reasonable explanation [of course I'm probably biased].
Note, "effective Born radius" has nothing to do with the surface
area/nonpolar calculation. It is---qualitatively anyway---the average
distance away from the solvent (i.e., where the dielectric constant
switches from 1 to 80). It would be worth familiarizing yourself with the
general theory of GB if this causes confusion. The Amber manual offers a
brief explanation with a number of references to look at for more detail.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Nov 19 2013 - 17:30:03 PST
