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

[Tsjerk Wassenaar]

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