> > Thanks for your response. But I could not understand some parts of your
> > answer. Let me explain how I look at this issue: The volume of a truncated
> > octahedron is defined as
> >
> > V = 11.3137085 * a^3
> >
> > in http://en.wikipedia.org/wiki/Truncated_octahedron
>
> Wikepedia is a source of information, however "truncated octahedron" can
> be defined in multiple ways. For example, look at the definition used in
> Allen & Tildesley which essentially lopes off corners of a cubic box
> compared to that implemented in AMBER (as a triclinic unit cell).
Dear Cheatham,
Thanks for your answers. I have a couple of other questions, regarding
this topic.
It is not so clear to me what u mean by "... however "truncated
octahedron" can be defined in multiple ways....". Do u mean that in a
different space where you have a different type of metric, the 'truncated
octahedron' can be defined different? Or do u mean that the volume of a
'truncated octahedron' can be defined in multiple ways?
> V = x * y * z * sqrt(1.0 - cos(alpha)**2 - cos(beta)**2 - cos(gamma)**2 +
> 2.0 * cos(alpha) * cos(beta) * cos(gamma))
>
Thanks for the .pdf file u sent. I am trying to understand/prove why the
volume is defined by the above equation. I saw a message of Dave Case in
the amber mailing list, where he is referencing a 1997 paper regarding
'truncated octahedrons'. As far as I understood, amber sim.s are done
using triclinic cells. And in order to use the truncated octahedral
solvation box, it is mapped to a triclinic cell (at least that is what I
understood). I would like to understand how this mapping is done.
Another question is, why to use triclinic cell? Is it hard to explicitly
use truncated octahedrals in the simulations? By combining triclinic
cells, someone can create a continous system; but this must be true for
combining truncated octahedrons, too.
> We discuss this in Current Protocols in Nucleic Acid Chemistry (articles
> by Cheatham, Kollman and Brooks) from ~2000-2003. See the attached PDF
> for a summary.
Unfortunately, our library does not have this journal. Can u give me the
full references of these papers published in this journal? I will ask from
the library to get it for me, but they need the full reference
information. Thanks again.
Best,
--
Ilyas Yildirim
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Received on Wed Jul 25 2007 - 06:07:42 PDT
