[gmx-users] Simulation Box type

[Mark Abraham]

On 17/07/2012 4:16 PM, tarak karmakar wrote:
> Dear All,
>
>
> I want to opt for the rhombic dodecahedron box in my simulation of a
> protein. I am using the following command to select the type of the
> box
> "editconf -f test.gro -o test_box.gro -c -d 1.2 -bt dodecahedron"
> but after this if I'm seeing this protein system within the box in VMD
> but its not showing that dodecahedron box, instead showing rectangular
> one. I don't know whether I am giving the wrong command or it's coming
> out from VMD software.
>     So can anyone give suggestion regarding this problem so that I can
> make myself confirmed by seeing the exact box, I need to have, prior
> to the simulation.

This is normal (discussed often in the archives). The box is specified 
by its vectors, not by the atomic coordinates, and the triclinic box you 
can see with VMD is equivalent to what you chose (e.g. a 2D tiling with 
hexagons can be represented as a 2D tiling of rhombuses). You can see 
trjconv -h about -ur to change the coordinates for visualization purposes.

Mark