Hi Tsjerk,<br><br>Thank you for all the clarifications. Just one more thing, I excluded the loop residues with RMSF>4 A. (because their movement is dominated by random diffusion), did PCA on the rest of the protein, and the cosine content improved significantly. Is this procedure acceptable?<br>
<br>Thanks in advance.<br>Thomas<br><br><br><br><div class="gmail_quote">On 6 April 2012 00:12, 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 Thomas,<br>
<br>
First of all, proteins in solution don't suddenly stop with Brownian<br>
motion at some point. It's just the way things move at the microscopic<br>
level. Second, the cosine content has nothing to do with randomness.<br>
Really. Nothing. On the contrary. The cosine content indicates<br>
unidirectional motion. I repeat, the cosine content has NOTHING to do<br>
with RANDOM motion! Really really. High cosine content?<br>
U-ni-di-rec-tio-nal motion; movement from one point to another point.<br>
The trick is realizing that the best reaction coordinate for random<br>
motion from point A to point B is the straight line between A and B.<br>
<br>
Unfortunately, the RMSIP is no help where it comes to convergence. It<br>
only tells you whether the directions in conformational space along<br>
which most of the motion takes place is similar between two (parts of)<br>
simulations. For convergence, you want to check the projections, and<br>
the cosine content thereof. The cosine content should indeed be low.<br>
Your case, with relatively high cosine content in every window,<br>
suggests that there is still motion, c.q. conformational<br>
rearrangement, on route to another state of the system. I fear there<br>
is no other way of looking at it that will suggest it has converged<br>
already. Actually, 20 ns is very little for equilibration, especially<br>
if convergence requires rearrangement of protein-protein interactions.<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br clear="all"><br></div></div></blockquote></div><br>-- <br>
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<p style="margin-bottom:0cm" align="LEFT">Thomas Evangelidis</p>
<p style="margin-bottom:0cm" align="LEFT">PhD student</p>
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Foundation, Academy of Athens</p>
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