[gmx-users] ED analysis

[Ruben M Buey]

I´ll do it!
Thanks a lot for your mails. They help me a lot!
with best wishes,
Ruben

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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-- 
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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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