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

[Quyen V. Vu]

> > 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
> > --
I read at somewhere that VMD hasn't support for dodecahedron box type yet and 
VMD will use a vector by the first three number for cubic dimension. 
Don't worry about that, your system still is dodecahedron