Hi,<br><br><div><span class="gmail_quote">On 5/23/06, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<a href="mailto:mernst@tricity.wsu.edu">mernst@tricity.wsu.edu</a> wrote:<br>> Hello fellow Gromacs-users,<br>><br>> Today I was extracting PDB snapshots from a solvated DNA 12mer simulation trajectory.<br>> When I went to view the snapshots, I saw that one of the DNA strands suddenly jumped
<br>> some nanometers away from its partner during certain frames. I remembered that there was<br>> a note about fixing this artifact in the trjconv documentation, and soon found that the<br>> -whole or -nojump options produced an easier-to-view snapshot series.
<br><br>Well done.</blockquote><div><br>
Hear, hear! :)<br>
</div> <blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>The simplest hypothesis for these images is that the visualisation<br>program is placing the first atom it finds in each molecule inside the
<br>box and the rest of it consistent with that placement. More visually<br>appealing might be an algorithm that located the center-of-mass<br>inside... shrug. Playing with the trjconv options before the<br>visualisation program gets into the mix may help here.
<br><br>Mark</blockquote><div><br>
In fact, it is Gromacs which uses the first atom to decide in which box
the molecule should be located during MD. But ALWAYS think of the
simulation system as an infinite tiling of simulation unit cells. It
doesn't matter a bit how you choose your single simulation cell from
that infinite system.., except for visualization.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
</div></div><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands
<br>+31 50 363 4336<br>