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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
