[gmx-users] Odd behaviour of editconf or VMD?

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Aug 30 10:24:40 CEST 2016

Hi Jernej,

This is simpler in two dimensions:
Consider a hexagonal unit cell.
Draw it, together with the surrounding copies (7 hexagons total).
Now connect the central hexagon with the right horizontal neighbor, and
with the 'northeast' neighbour.
Connect these two neighbors with their other common neighbor.
You drew a parallelogram.
Check that the contents of the parallelogram is the same as that of any
Now think of how it works with a rhombic dodecahedron and a parallelepiped.



On Tue, Aug 30, 2016 at 10:17 AM, Jernej Zidar <jernej.zidar at gmail.com>

> Hi,
>   I am trying to solvate a small DNA molecule. Since I don't want so
> simulate more waters than what is really neccessary, I decided to try the
> dodecahdron and octahedron unit cells.
>   After I added waters I went to examine the resulting structures in VMD
> only to find that the octahedron and dodecahedron cells are completely
> wrong. Instead of the familiar shape (roughly a cube with trimmed edges for
> dodeachedron), I am greeted with a parallelepiped-like shape.
>   I tried Gromacs 5.0.7, 5.1.3, 2016 but the results seem to be always the
> same. Is this an expected behaviour? How do I "reconstitute" the resulting
> structure?
> Thanks,
> Jernej
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Tsjerk A. Wassenaar, Ph.D.

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