Hello sir, <br><br>I had used a dodecahedron cell for simulation. I have run<br>the simulation for 100ns, did you man I have to restart the<br>simulation again?<br><br>Thanking you<br>Kavya <br><br><div class="gmail_quote">
On Sun, May 29, 2011 at 5:40 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>
> "shortest periodic distance is 1.39714 (nm) at time 21824 (ps),<br>
> between atoms 2062 and 3688"<br>
> where 2062 is a protein atom and 21824 is a water molecule.<br>
<br>
</div>21824 is the time in ps at which the two atoms indicated, 2062 and<br>
3688, are at the short distance given. You can dump the frame with<br>
trjconv and have a look. Probably your molecule stretched, or you<br>
solvated in a rectangular box and the protein rotated. In the first<br>
case, set a larger distance, in the second, use a rhombic<br>
dodecahedron.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br>
<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>
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