On 12/17/12 3:04 PM, zugunder wrote:
Justin Lemkul wrote
It is calculated correctly, the math is just a bit more complex (see the
manual for the equations). The distance to the box edge is defined the
same way, but the two approaches don't necessarily give equally suitable
results. Consider the first case, which produces a rectangular box from
an elongated configuration. If your protein rotates 90 degrees about the
z-axis, you will likely violate the minimum image convention, as the box
vector along y is insufficient to accommodate the protein. Problem! The
dodecahedral box is pseudo-spherical and thus, regardless of how the
protein rotates, the minimum image convention is not violated.
So, in other words, the safest way for an elongated protein (with no
restrictions on rotation) is either a cube or dodecahedron, because only in
these 2 cases only the longest dimension of the protein is effectively taken
into account - do I understand it correctly? And obviously, this is true for
any almost-spherical protein as well...
Yes, it's a reflection on the inherent rotational symmetry of the molecule. A
dodecahedron can give you the same periodic distance as a cube, but is much more
efficient since there are fewer waters.
And, therefore, any rectangular box, different from a cube will bring to a
violation of the minimum image convention in case of unrestricted rotation
of an elongated protein around its shorter axes assuming we set the same -d
as in case of a cube? So do I get it right that non-cubic rectangular boxes
are used only in such specific cases with restrictions on rotation?
Or in cases where a rectangle is suitable, i.e. for surfaces or membranes.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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