[gmx-users] ED analysis

Ruben M Buey ruben at akilonia.cib.csic.es
Tue Sep 7 14:52:38 CEST 2004

Hi all,
If I have calculated them correctly (g_anaeig ... -proj proj1.xvg -first 
1 -last 1, and so on for eigenv 2,3,4 and 5; g_analyze -f proj1.xvg -cc 
and so on...), the cosine contents are:
eigenv 1:       0.849
           2:       0.012
           3:       0.0029
           4:       7.96e-6
           5:       0.00072

Does it mean that the first eigenvector is a ramdom diffusion effect and 
the other are significant movements? Anyway I can see only very small 
diferences in the eigenvector 2 for the two extreme structures...
Thanks a lot for your help,

Berk Hess wrote:

>> From: Ruben M Buey <ruben at akilonia.cib.csic.es>
>> To: gmx3 at hotmail.com, vdava at davapc1.bioch.dundee.ac.uk
>> Subject: Re: [gmx-users] ED analysis
>> Date: Mon, 06 Sep 2004 15:18:49 +0200
>> Berk and Daan,
>> Thanks a lot for the reply.
>> Just to make sure... (sorry for disturbing). I attach the graph just 
>> to check if the "semi-circumference shape" could be due to ramdom 
>> diffusion as Berk has just  pointed.
> I would say typical random diffusion effect.
> Your simulation is probably way to short to see any convergence
> for the first few principal modes.
> But please read the ref's given in the manual.
> You can do two simple checks:
> Do PCA on the first and second half of the trajectory and compare
> the eigenvectors with g_anaeig to see if there is any convergence.
> And check the cosine content of the first few eigenvectors: g_anaeig -cc
> Berk.
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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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