Dear Sir, <br><br> Thank you sir for the clarification. But if there is only one<br>polymer (protein) with water in the system then also is it <br>necessary because in one of the mails -<br><a href="http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html">http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html</a><br>
there was a discussion regarding this topic. So I wanted to<br>ensure regarding that<br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">It is absolutely necessary that the molecules be whole, and in the<br>
case of multimers, correctly assembled.<br></blockquote><div><br>But if there is only one
polymer (protein) with water in the system <br>then also is it
necessary to use nojump or mol in trjconv?because<br>in one of the mails -<br>
<br><a href="http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html">http://lists.gromacs.org/pipermail/gmx-users/2010-October/055320.html</a><br>
<br>there was a discussion regarding this topic. So I wanted to<br>
ensure regarding that aspect. Molecule after simulation <br>crosses the box boundary in the simulation I have done, So<br>if I processed analyzing with the native .xtc file there will be <br>a problem? But in this case its a single intact protein molecule<br>
in water.<br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Worse, the first eigenvector can be dispersed over the second and<br>
third in another (equivalent) system. But this is what the RMSIP is<br>
for. It is a measure to indicate how much one set of eigenvectors<br>
corresponds to another, regardless of the order.<br></blockquote><div> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
Yes, it is absolutely necessary that the conformational space is<br></div>
defined in the same way for the different systems. Let's say you have<br>
a set of configurations X, for which you determine the covariance<br>
matrix and the eigenvectors/-values:<br>
<br>
S = (1/N)XX' = PDP'<br>
<br>
Now take the same system, but rotated:<br>
<br>
T = (1/N)RXX'R' = RPDP'R'<br>
<br>
So the eigenvectors for the rotated configurations are rotated too.<br></blockquote><div> </div><div>Ok.<br> </div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">
> 4. Kindly provide a clear protocol for the essential dynamics<br>
> analysis of 4 proteins with different sequence length and<br>
> sequence similarity. but the native structures superpose<br>
> very well 3 dimensionally.<br>
<br>
</div>This is up to you... Sorry.<br></blockquote><div> </div><div>I will find a way. Thank you sir..<br></div></div><br>Thanking you<br>With Regards<br>M. Kavyashree<br>