[gmx-users] Periodic Images - clarification

[Tsjerk Wassenaar]

Hi Kavya,

> I did use dodecahedron cell.  but how does using a dodecahedron cell
> be advantageous than any other cell when minimum image violation
> has occurred? This is just my inquisitiveness.

In a rectangular cell, such interactions may occur merely by
reorientation of the solute. In that case it is likely that
self-interactions over PBC have a persistent effect on the dynamics.

> And when I was visualizing
> the trajectory in VMD along with other periodic images in +/-X, +/-Y and
> +/-Z
> directions I saw only 26images, this is good for a cubic cell. But how
> can I visualize a dodecahedron cell? Which has more faces ---> more periodic
> images (If I am not wrong) than a cubic or rectangular cell..

Actually, there are less. A rhombic dodecahedron has 12 neighbours. A
cubic/rectangular cell has 6 faces, but for those you also have to
consider the neighbours at the edges and corners, which brings the
total to 26.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands