Hi Nahren. > > I have run my simulation for 12 ns (of a protein dimer ).. I see the box > remain octahedron till about 5 ns after that the sides of the dodecahedron > becomes unequal. > i tried -pbc atom/whole etc, but does not help. > Any advice on the issue will be truly helpful. > > regards, > nahren > > An octahedron is not the same as a dodecahedron. Besides there's noteworthy distinction between octahedron and _truncated_ octahedron and between dodecahedron and _rhombic_ dodecahedron.
If you use anisotropic or semi-isotropic pressure coupling, you're box may skew and the sides from the shape resulting from using -pbc compact will not be equal anymore. In fact, your initial _regular_ rhombic dodecahedron will become a _general_ rhombic dodecahedron (and any unit cell can be represented as a general rhombic dodecahedron). Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
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