[gmx-users] The octahedron problem

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 19 13:22:46 CEST 2015

Hi Tuong Vy,

An octahedral or dodecahedral box is pretty tricky. I have a Pymol script
for generating them, but it will probably require some more work...


On May 19, 2015 13:18, "Vy Phan" <phanvy120690 at gmail.com> wrote:

> Dear Gromacs Users,
> I have the problem with generating the octahedron box.  I always get the
> rectangular box (using VMD)
> When I searched on the gmx maillist, I saw some people met same problem.
> Is problem is normal in gromacs?
> After run simulation, I can display the trajectory on VMD by using the
> command trjconv -pbc mol -ur compact for converting the system. But I can
> not display the octahedron box after solvated system.
> Could someone help me ?
> Tuong Vy
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