Dear Sir,<br><br>1 simulation for 100ns -<br>ED analysis proceeded as follows:<br><br>g_covar -s <input>.tpr -f .<input>.xtc -o eigenvectors.xvg -v eigenvalues.trr -xpma covar.xpm<br>g_anaeig -s <input>.tpr -f <input>.xtc -v eigenvectors.trr -eig
eigenvalues.xvg -proj proj-evi.xvg -extr evi.pdb
-rmsf rmsf-evi.xvg -first i -last i<br>(here i refers to the eigen vector index)<br>Thus generated 5 eigen vectors.<br><br>Visualised the trajectory along these eigen vectors using<br><br>g_nmtraj -s <input>tpr -v eigenvector.trr -o <output>pdb -eigen i -phases x -temp x -amplitude x -nframes x<br>
(i referes to eigen vectors. In this I was not clear about the significance of phases, amplitude)<br><br>I visualised the pbd output in pymol there was very minute movement of some loop regions.<br><br>on the other side-<br>
When I visualised the .xt file output as pdb according to Dr.Tjerk's tutorial or<br>by superposing all the structures in trajectory over initial structure in pymol<br>there was a significant degree of movement in those loops.<br>
<br>so my question here is why these two does not correlate. I agree that trajectory<br>along one eigenvector might not give movements of all the regions that is observed<br>in superposed trajectory but whichever region it shows movements is extremely less<br>
compared to that when viewed from superposed structures in trajectory.<br><br>I hope this is not confusing.<br><br>Thanking you<br>With regards<br>M, Kavyashree<br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 1:27 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>
<br>
For us to say anything sensible about it, we should at least know<br>
exactly what you've tried. Copy-paste the commands exactly as you<br>
issued them, and provide the parts of the output that seem relevant.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div></div><div class="h5"><br>
On Thu, Jun 23, 2011 at 9:54 AM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
> Dear Sir,<br>
><br>
> I tried fitting the proteins of the trajectory in pymol<br>
> as mentioned in your (Dr. Tsjerk's) tutorial, but later<br>
> I tried using the trjconv -fit rot+trans to fit the proteins<br>
> in the trajectory as you had mentioned.<br>
><br>
> I do not observe this degree of movement in protein<br>
> when I view the trajectory along any 1-5 eigen vectors.<br>
> This trajectory along any of these eigen vector is very minute<br>
> and cannot be compared to that obtained after superposing<br>
> the structure in the trajectory. Why is it so?<br>
> Please let me know if I am understanding the concept wrong.<br>
><br>
> Thanking you<br>
> With regards<br>
> M. Kavyashree<br>
><br>
><br>
> On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
>><br>
>> Thank you Sir!<br>
>><br>
>> With regards<br>
>> M. Kavyashree<br>
>><br>
>> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
>> wrote:<br>
>>><br>
>>> trjconv -fit rot+trans<br>
>>><br>
>>> Cheers,<br>
>>><br>
>>> Tsjerk<br>
>>><br>
>>> On Jun 23, 2011 8:12 AM, "Kavyashree M" <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
>>><br>
>>> Dear Users,<br>
>>><br>
>>> Are there any tool for superposing the trajectory<br>
>>> structures form MD. Please correct me if I am asking<br>
>>> any illogical question.<br>
>>> My previous question was regarding the trjconv output<br>
>>> pdb trajectory, is there a way to superpose all these<br>
>>> structures?<br>
>>><br>
>>> Thank you<br>
>>> With regards<br>
>>> M. Kavyashree<br>
>>><br>
>>> On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
>>> > > Dear users, > > I...<br>
>>><br>
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<br>
--<br>
</div></div>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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