AMBER Archive (2003)

Subject: Re: octahedral volume

From: David A. Case (case_at_scripps.edu)
Date: Tue Jan 21 2003 - 11:03:23 CST

On Fri, Jan 17, 2003, Peter Varnai wrote:
>
> When constructing the system, leap reports a volume. This has
> been changed between version 6 and 7 according to leap/tools.c:
> dVolume = dMaxX * dMaxY * dMaxZ;
> ver6:
> dVolume *= 0.5;
> ver7:
> dVolume *= 0.7698004;
> /* = sqrt(1 - 3*cost^2 - 2*cost^3), where cost = -1/3 = cos(109.471) */
>
> Can someone explain where the ver7 formula comes from?

Between 6 and 7, amber changed the way it internally handles truncated
octahedra. The new way uses an equivalent triclinic cell; this doesn't
"look" like a truncated octahedron, but is equivalent to it. The ptraj
"image" command knows how to rearrange the boundaries to look like the
truncated octahedron.

I'm not an expert on this stuff, and maybe others can chime in. But I
think the basic ideas are given in the following paper (among other places):

%A H. Bekker
%T Unification of Box Shapes in Molecular Simulations.
%J J. Computat. Chem.
%V 18
%P 1930-1942
%D 1997

..dac 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================