[gmx-users] ED analysis

Daan van Aalten vdava at davapc1.bioch.dundee.ac.uk
Mon Sep 6 14:43:34 CEST 2004

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.
"A comparison of techniques for calculating protein ssential dynamics"
J.Comp.Chem. (1997), 18, 169-181.

hope this helps



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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