[gmx-users] ED analysis

Ruben M Buey ruben at akilonia.cib.csic.es
Mon Sep 6 17:49:03 CEST 2004

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

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.
> _________________________________________________________________
> Play online games with your friends with MSN Messenger 
> http://messenger.msn.nl/
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.

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

More information about the gromacs.org_gmx-users mailing list