On Mon, Jul 16, 2012 at 4:03 PM, Yun Shi <yunshi09.gmail.com> wrote:
> So what does "idiv" stands for (sorry I did not find this in manual)?
>
idiv is the dividing factor for the barrier height. Think of it as the
'multiplicity' of the dihedral (i.e., how many times that dihedral appears).
As a simple example, think of ethane, and the one dihedral in that system
(namely the one around the C-C bond). What you could envision doing is
calculating the potential energy surface around that dihedral using quantum
mechanics and using the force field with just the 1-4 non-bonded
interactions defining the potential (that is, we haven't yet added a
dihedral term). We can fit dihedral terms to that difference to get our
required barrier height, phase, periodicity, etc.
However, there is a detail you need to account for here. You have the
necessary term(s) for the entire dihedral, but LEaP will recognize 9 such
dihedrals! Each C has 3 hydrogen atoms, so LEaP will define 9 distinct
dihedrals ALL matching H-C-C-H involving rotation around that one C-C bond.
Therefore, you have to divide the barrier height by 9 when you add each
dihedral together. As a general rule, you can always set idiv=1 as long as
you divide the barrier height appropriately (indeed, when extracting
parameters from a topology file, this is the only way you can present the
data), but this mechanism is in place to help FF developers, I imagine.
Why not just use pk/idiv as the pk value in amber ff?
>
Hopefully answered above.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 16 2012 - 14:00:03 PDT
