Dear Sir, <br><br>I did use dodecahedron cell. <br><br><div class="gmail_quote">On Mon, Jun 27, 2011 at 12:35 AM, 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;">Hey,<br>
<br>
Maybe I missed this, but what type of unit cell did you use? You<br>
should use a rhombic dodecahedron.<br></blockquote><div><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. And when I was visualizing<br>
the trajectory in VMD along with other periodic images in +/-X, +/-Y and +/-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><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Then, I would argue that it isn't necessarily so problematic as the<br>
others put it when you have transient contacts. For the greater part<br>
of the simulation the distances in the periodic system are so large<br>
that there can be no direct effect between opposite ends of the<br>
protein. It is unlikely that the brief periods where the opposite ends<br>
were within each others sphere of influence - not in contact - would<br>
have caused a persistent deviation from in ensemble. Mind that it's<br>
not wrong that a protein would suddenly feel some presence from some<br>
end of a similar protein some distance away at some time. It's just<br>
wrong if a protein aligns with itself. That has not happened if these<br>
minimal distances were only transient. It may well be that the protein<br>
was going from one conformation to another, for which it had to go<br>
through something that would violate the PBC a bit. Still, you are in<br>
for some discussion, and have to argue, based on what the simulation<br>
shows you, what (a) replicate simulation(s) show(s) you and what you<br>
know of your protein, why it would be justified to draw conclusions<br>
based on that trajectory.<br>
<br>
But those are just my two cents.<br></blockquote><div><br>Thanks for the suggestions sir. I will be verify this with the dimer (disulphide<br>bonded) and monomer in a larger box size. <br><br></div>Thanking you<br>With Regards<br>
M. Kavyashree<br></div><br>