[gmx-users] About using dodecahedron in editconf

[David van der Spoel]

qiwenpeng at sinap.ac.cn wrote:

> Hello everyone!
> I use gromacs3.3/2.1 to simulate a DNA molecule. I want to use a box
> with a xy-hexagon to reduce the calculate time spenting.as follows:
> editconf -f 1.gro -o 2.gro -bt dodecahedron -box 2.5 2.5 10.5 -angles
> 60 60 60
> But the result is:
> the program say:
> Volume: 22.8935 nm^3, corresponds to roughly 10300 electrons No
> velocities found
> system size : 2.139 2.286 4.242 (nm)
> diameter : 4.391 (nm)
> center : 0.000 0.000 -0.000 (nm)
> box vectors : 2.403 4.144 2.299 (nm)
> box angles : 90.00 90.00 90.00 (degrees)
> box volume : 22.89 (nm^3)
> shift : 1.875 1.875 0.884 (nm)
> new center : 1.875 1.875 0.884 (nm)
> new box vectors : 2.500 2.500 2.500 (nm)
> new box angles : 60.00 60.00 90.00 (degrees)
> new box volume : 11.05 (nm^3)
> It is obvious wrong!

You can not have a dodecahedron with different box edges. You will have
to find the best triclinic box matching your requirements of
periodicity. Probably an elongated rectangle has the same effect.

Do remember that in a box like you want the DNA should not be allowed to
rotate, you'll have to turn this off explicitly.

> what can I do !!
> Thanks a lot
>
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