[gmx-users] rhombic dodecahedron membrane simulations

Krzysztof Murzyn ubmurzyn at cyf-kr.edu.pl
Fri Aug 22 12:50:01 CEST 2003

Hi all,

I'd like to perform an MD simulation of a lipid bilayer system using 
rhombic dodecahedron periodic boundary conditions. My starting 
configuration is in a rectangular box with dimensions, say, a, b and c 
(a != b != c). I guess I should use editconf with -box A B C -angles 60 
60 60; however, to preserve box volume new box dimensions must be 
somewhat bigger (by factor 1/sin(60) or so?).

Could someone give me any tips how to convert a rectangular box into a 
rhombic dodecahedron box?


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