Dear Sir, Yes it is not stated in your tutorial. I was mentioning about the superposition of trajectory and visualization in pymol. Ok I will try that. Thank you for the suggestions sir.
Thanking you With Regards M. Kavyashree On Thu, Jun 23, 2011 at 2:43 PM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Kavya, > > For certain I do not state in my tutorial that one should use g_nmtraj > for this. It is intended for analysis of normal modes analysis, where > the eigenvalues are related to the frequencies of the harmonic > motions. You're using it on the modes with largest eigenvalues, which > are interpreted as high frequencies, consequently giving small > amplitudes. This explains that you're not seeing much. > > To get an idea of the extent of the motion, look at the extreme > projections. To see how the trajectory moves along a certain mode, use > g_anaeig -filt > > Cheers, > > Tsjerk > > On Thu, Jun 23, 2011 at 10:56 AM, Kavyashree M <hmkv...@gmail.com> wrote: > > Dear Sir, > > > > 1 simulation for 100ns - > > ED analysis proceeded as follows: > > > > g_covar -s <input>.tpr -f .<input>.xtc -o eigenvectors.xvg -v > > eigenvalues.trr -xpma covar.xpm > > 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 > > (here i refers to the eigen vector index) > > Thus generated 5 eigen vectors. > > > > Visualised the trajectory along these eigen vectors using > > > > g_nmtraj -s <input>tpr -v eigenvector.trr -o <output>pdb -eigen i > -phases x > > -temp x -amplitude x -nframes x > > (i referes to eigen vectors. In this I was not clear about the > significance > > of phases, amplitude) > > > > I visualised the pbd output in pymol there was very minute movement of > some > > loop regions. > > > > on the other side- > > When I visualised the .xt file output as pdb according to Dr.Tjerk's > > tutorial or > > by superposing all the structures in trajectory over initial structure in > > pymol > > there was a significant degree of movement in those loops. > > > > so my question here is why these two does not correlate. I agree that > > trajectory > > along one eigenvector might not give movements of all the regions that is > > observed > > in superposed trajectory but whichever region it shows movements is > > extremely less > > compared to that when viewed from superposed structures in trajectory. > > > > I hope this is not confusing. > > > > Thanking you > > With regards > > M, Kavyashree > > > > On Thu, Jun 23, 2011 at 1:27 PM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: > >> > >> Hi Kavya, > >> > >> For us to say anything sensible about it, we should at least know > >> exactly what you've tried. Copy-paste the commands exactly as you > >> issued them, and provide the parts of the output that seem relevant. > >> > >> Cheers, > >> > >> Tsjerk > >> > >> On Thu, Jun 23, 2011 at 9:54 AM, Kavyashree M <hmkv...@gmail.com> > wrote: > >> > Dear Sir, > >> > > >> > I tried fitting the proteins of the trajectory in pymol > >> > as mentioned in your (Dr. Tsjerk's) tutorial, but later > >> > I tried using the trjconv -fit rot+trans to fit the proteins > >> > in the trajectory as you had mentioned. > >> > > >> > I do not observe this degree of movement in protein > >> > when I view the trajectory along any 1-5 eigen vectors. > >> > This trajectory along any of these eigen vector is very minute > >> > and cannot be compared to that obtained after superposing > >> > the structure in the trajectory. Why is it so? > >> > Please let me know if I am understanding the concept wrong. > >> > > >> > Thanking you > >> > With regards > >> > M. Kavyashree > >> > > >> > > >> > On Thu, Jun 23, 2011 at 11:56 AM, Kavyashree M <hmkv...@gmail.com> > >> > wrote: > >> >> > >> >> Thank you Sir! > >> >> > >> >> With regards > >> >> M. Kavyashree > >> >> > >> >> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar < > tsje...@gmail.com> > >> >> wrote: > >> >>> > >> >>> trjconv -fit rot+trans > >> >>> > >> >>> Cheers, > >> >>> > >> >>> Tsjerk > >> >>> > >> >>> On Jun 23, 2011 8:12 AM, "Kavyashree M" <hmkv...@gmail.com> wrote: > >> >>> > >> >>> Dear Users, > >> >>> > >> >>> Are there any tool for superposing the trajectory > >> >>> structures form MD. Please correct me if I am asking > >> >>> any illogical question. > >> >>> My previous question was regarding the trjconv output > >> >>> pdb trajectory, is there a way to superpose all these > >> >>> structures? > >> >>> > >> >>> Thank you > >> >>> With regards > >> >>> M. Kavyashree > >> >>> > >> >>> On Wed, Jun 22, 2011 at 10:52 PM, Kavyashree M <hmkv...@gmail.com> > >> >>> wrote: > >> >>> > > Dear users, > > I... > >> >>> > >> >>> -- > >> >>> gmx-users mailing list gmx-users@gromacs.org > >> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >>> Please search the archive at > >> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> >>> Please don't post (un)subscribe requests to the list. Use the > >> >>> www interface or send it to gmx-users-requ...@gromacs.org. > >> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >>> > >> >>> -- > >> >>> gmx-users mailing list gmx-users@gromacs.org > >> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >>> Please search the archive at > >> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> >>> Please don't post (un)subscribe requests to the list. Use the > >> >>> www interface or send it to gmx-users-requ...@gromacs.org. > >> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> > >> > > >> > > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > Please search the archive at > >> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > >> > >> > >> > >> -- > >> Tsjerk A. Wassenaar, Ph.D. > >> > >> post-doctoral researcher > >> Molecular Dynamics Group > >> * Groningen Institute for Biomolecular Research and Biotechnology > >> * Zernike Institute for Advanced Materials > >> University of Groningen > >> The Netherlands > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > * Groningen Institute for Biomolecular Research and Biotechnology > * Zernike Institute for Advanced Materials > University of Groningen > The Netherlands > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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