[gmx-users] rhombic dodecahedron construction
Trayder Thomas
trayder.thomas at monash.edu
Fri May 23 04:42:57 CEST 2014
Hi,
I'm trying to figure out how to construct a rhombic dodecahedron for a
membrane system.
The manual (Section 3.2.1) states:
"There are two different orientations of a rhombic dodecahedron that
satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the
orientation which has a square intersection with the xy-plane. This
orientation was chosen because the first two box vectors coincide with the
x and y-axis, which is easier to comprehend. The other orientation can be
useful for simulations of membrane proteins. In this case the cross-section
with the xy-plane is a hexagon, which has an area which is 14% smaller than
the area of a square with the same image distance. The height of the box
(cz) should be changed to obtain an optimal spacing."
I can't figure out how to construct the system with a hexagon on the x-y
plane, I presume I can rotate the box but I can only visualise the result
as a triclinic cell.
I also can't figure out how to adjust the height of the box, editconf only
accepts a single magnitude for dodecahedron vector lengths.
Any help would be greatly appreciated.
Thanks in advance,
-Trayder
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