Dear Sir<br><br>Thanks I got the point!<br><br>Thanking you<br>With Regards<br>M. Kavyashree<br><br><div class="gmail_quote">On Mon, Jun 27, 2011 at 12:19 PM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Kavya,<br>
<div class="im"><br>
> I did use dodecahedron cell. but how does using a dodecahedron cell<br>
> be advantageous than any other cell when minimum image violation<br>
> has occurred? This is just my inquisitiveness.<br>
<br>
</div>In a rectangular cell, such interactions may occur merely by<br>
reorientation of the solute. In that case it is likely that<br>
self-interactions over PBC have a persistent effect on the dynamics.<br>
<div class="im"><br>
> And when I was visualizing<br>
> the trajectory in VMD along with other periodic images in +/-X, +/-Y and<br>
> +/-Z<br>
> directions I saw only 26images, this is good for a cubic cell. But how<br>
> can I visualize a dodecahedron cell? Which has more faces ---> more periodic<br>
> images (If I am not wrong) than a cubic or rectangular cell..<br>
<br>
</div>Actually, there are less. A rhombic dodecahedron has 12 neighbours. A<br>
cubic/rectangular cell has 6 faces, but for those you also have to<br>
consider the neighbours at the edges and corners, which brings the<br>
total to 26.<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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