[gmx-users] Periodic Images - clarification

[Kavyashree M]

Dear Sir

Thanks I got the point!

Thanking you
With Regards
M. Kavyashree

On Mon, Jun 27, 2011 at 12:19 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>wrote:

> 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
> --
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