[gmx-users] center of dodecahedron

[Mark Abraham]

On Jan 26, 2014 9:30 AM, "Mahboobeh Eslami" <mahboobeh.eslami at yahoo.com>
wrote:
>
> hi GMX users
> i simulate protein ligand complex in dodecahedron box
> when i use following command
>
> editconf -f complex.pdb -o newbox.gro -bt dodecahedron -d 1.0 -c
> My complex is not located in the center of box,
>
> How do I put the complex  in the center of box?

It is in the center of the dodecahedral cell, but not in the triclinic
representation of that cell, which is the default output representation.
See
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditionsfor
info and suggestions on using trjconv to get the visual confirmation
you seek.

Mark

> thanks for your's help
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