[gmx-users] octahedron box shape problem

[Erik Lindahl]

thomas stockner wrote:

> Hi
>
> I am trying to generate an octahedron or dodecahedron box for a MD
> simulation, but unfortunately I  am not succesful. I get only rectangular
> boxes.
>
> I am using Gromacs version 3.0.5
>
> applying a commands like:
> -editconf -f struc.g96 -o box.g96 -d 1.4 -bt octahedron -label A
> -genbox -cp box.g96 -cs spc216.gro -o h2o.g96 -p struc.top
> and creating a pdb file for visualizing with rasmol
> -pdb2gmx -f h2o.g96 -o rasmol.pdb
> the box I get is always recangular, independenty which options of editconf I
> tryed (-bt; -angles; -box).
> I don't understand, why the output of editconf regarding the box statistic
> does not correspond to characteristics of the filled water box of the pdb
> file visualised with rasmol.
>
> I cannot find the error I make. Could anyone help me to generate an
> octahedron box.

Hi Thomas,

What does the last line of the .gro file look like? If there are nine numbers
and more than three of them are non-zero the box is probably correct.


I don't know right off, but one possibility is that the gromacs box
really is an octahedron but it doesn't show in your viewer program.

ngmx can show the different box types if you select it from one of
the menus. Note however that the water molecules might not all
be drawn within the box before you have performed any simulation,
and that might cause it to look like the box isn't right.

Cheers,

Erik