[gmx-users] ED analysis

[Berk Hess]

If almost no motion can be observed, as Ruben reported,
it does not mean a curved trajectory.
Random diffusion in a few dimensions produces a half and
a full cosine as first two principal components:
p1(t) = A cos(pi t/t_total)
p2(t) = A/2 cos(2 pi t/t_total)
Together these give the "pretty semi-circumference shape".

>From: Daan van Aalten <vdava at davapc1.bioch.dundee.ac.uk>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Ruben M Buey <ruben at akilonia.cib.csic.es>
>CC: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] ED analysis
>Date: Mon, 6 Sep 2004 13:43:34 +0100 (BST)
>
>
>Hi Ruben
>
>This usually means that the two eigenvectors together describe a motion
>with a curved trajectory of atoms. This turns out to be a major limitation
>of Cartesian-coordinate-based ED - single eigenvectors can only describe
>(by definition) linear motions in hyperspace. Thus, if you have a two
>domain protein, and one of these domains shows a significant hinge bending
>motion (i.e. atoms describe curves in 3D space) then a Cartesian ED
>analysis can simply not "catch" that in a single eigenvector.
>
>Switching to ED in torsion angle space *seems* an obvious improvement -
>but there are a few problems associated with this - see
>D.M.F. van Aalten, B.L. de Groot, J.B.C. Findlay, H.J.C. Berendsen and A.
>Amadei
>"A comparison of techniques for calculating protein ssential dynamics"
>J.Comp.Chem. (1997), 18, 169-181.
>
>hope this helps
>
>cheers
>
>Daan
>
>On Mon, 6 Sep 2004, Ruben M Buey wrote:
>
> > Hi all,
> > Just a novice´s question about ED analysis.
> > What does it mean when I get a nice correlation between the projections
> > onto the eigenvectors 1 and 2 of a MD trajectory?
> > Actually the graph has a pretty semi-circumference shape... when I look
> > at the extreme projections over these eigenvectors, I can only see
> > really small diferences between the structures but no domain movements
> > or collective motions. How can I look at this?
> > Thanks in advance for your kind atention,
> > with bests regards,
> > Ruben
> >
> > --
> > ------------------------------------------------------
> > Ruben M Buey. PhD student. Lab 308
> > Centro de Investigaciones Biologicas
> > Consejo Superior de Investigaciones Cientificas
> > Dpt. Protein Function and Structure
> > C/ Ramiro de Maeztu, 9
> > 28040  Madrid   (SPAIN)
> > Phone:   34-918373112 ext 4380
> > Fax:     34-915360432
> > ------------------------------------------------------
> >
> >
> >
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