Dear Sir, <br><br>Yes it is not stated in your tutorial. I was mentioning <br>about the superposition of trajectory and visualization <br>in pymol. <br>Ok I will try that. Thank you for the suggestions sir. <br><br>Thanking you<br>
With Regards<br>M. Kavyashree<br><br><br><br><br><div class="gmail_quote">On Thu, Jun 23, 2011 at 2:43 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 certain I do not state in my tutorial that one should use g_nmtraj<br>
for this. It is intended for analysis of normal modes analysis, where<br>
the eigenvalues are related to the frequencies of the harmonic<br>
motions. You're using it on the modes with largest eigenvalues, which<br>
are interpreted as high frequencies, consequently giving small<br>
amplitudes. This explains that you're not seeing much.<br>
<br>
To get an idea of the extent of the motion, look at the extreme<br>
projections. To see how the trajectory moves along a certain mode, use<br>
g_anaeig -filt<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="h5"><br>
On Thu, Jun 23, 2011 at 10:56 AM, Kavyashree M <<a href="mailto:hmkvsri@gmail.com">hmkvsri@gmail.com</a>> wrote:<br>
> 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<br>
> eigenvalues.trr -xpma covar.xpm<br>
> g_anaeig -s <input>.tpr -f <input>.xtc -v eigenvectors.trr -eig<br>
> eigenvalues.xvg -proj proj-evi.xvg -extr evi.pdb -rmsf rmsf-evi.xvg -first i<br>
> -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<br>
> -temp x -amplitude x -nframes x<br>
> (i referes to eigen vectors. In this I was not clear about the significance<br>
> of phases, amplitude)<br>
><br>
> I visualised the pbd output in pymol there was very minute movement of some<br>
> loop regions.<br>
><br>
> on the other side-<br>
> When I visualised the .xt file output as pdb according to Dr.Tjerk's<br>
> tutorial or<br>
> by superposing all the structures in trajectory over initial structure in<br>
> 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<br>
> trajectory<br>
> along one eigenvector might not give movements of all the regions that is<br>
> observed<br>
> in superposed trajectory but whichever region it shows movements is<br>
> 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>
> On Thu, Jun 23, 2011 at 1:27 PM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
>><br>
>> 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>
>><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>><br>
>> > 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>><br>
>> >>> wrote:<br>
>> >>> > > Dear users, > > I...<br>
>> >>><br>
>> >>> --<br>
>> >>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> >>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> >>> Please search the archive at<br>
>> >>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>> >>> Please don't post (un)subscribe requests to the list. Use the<br>
>> >>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> >>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>> >>><br>
>> >>> --<br>
>> >>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> >>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> >>> Please search the archive at<br>
>> >>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>> >>> Please don't post (un)subscribe requests to the list. Use the<br>
>> >>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> >>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>> >><br>
>> ><br>
>> ><br>
>> > --<br>
>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> > Please search the archive at<br>
>> > <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>> > Please don't post (un)subscribe requests to the list. Use the<br>
>> > www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> > Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> 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>
>> --<br>
>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
>> Please search the archive at<br>
>> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
>> Please don't post (un)subscribe requests to the list. Use the<br>
>> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
>> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
><br>
> --<br>
> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at<br>
> <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
><br>
<br>
<br>
<br>
--<br>
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>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>