[gmx-users] Re: Trajectory and ED - (not old question again)

Thu Jun 23 12:48:48 CEST 2011

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 <tsjerkw at 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 <hmkvsri at 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 <tsjerkw at 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 <hmkvsri at 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 <hmkvsri at gmail.com>
> >> > wrote:
> >> >>
> >> >> Thank you Sir!
> >> >>
> >> >> With regards
> >> >> M. Kavyashree
> >> >>
> >> >> On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar <
> tsjerkw at gmail.com>
> >> >> wrote:
> >> >>>
> >> >>> trjconv -fit rot+trans
> >> >>>
> >> >>> Cheers,
> >> >>>
> >> >>> Tsjerk
> >> >>>
> >> >>> On Jun 23, 2011 8:12 AM, "Kavyashree M" <hmkvsri at 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 <hmkvsri at gmail.com>
> >> >>> wrote:
> >> >>> > > Dear users, > >    I...
> >> >>>
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> >> --
> >> 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
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>
>
> --
> 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
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