[gmx-users] Odd behaviour of editconf or VMD?
Quyen V. Vu
vuqv.phys at gmail.com
Tue Aug 30 14:06:33 CEST 2016
> > 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
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