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

[Kavyashree M]

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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