[gmx-users] About using dodecahedron in editconf

[qiwenpeng at sinap.ac.cn]

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!

what can I do !!

Thanks a lot

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