[gmx-users] PCA mathematical information

Wes Barnett w.barnett at columbia.edu
Wed Feb 7 18:16:54 CET 2018

On Tue, Feb 6, 2018 at 5:11 AM, edesantis <edesantis at roma2.infn.it> wrote:

> Dear gromacs users,
> I am a PhD student in biophysics,
> I am trying to preform principal component analysis on my simulations with
> the aim to understand if there are present correlated motions during the
> dynamics.
> I an not expert of this kind of analysis,
> I was studying different tutorials and I saw that it is common to filter
> the trajectory to show only the motion along some eigenvectors  (gmx anaig
> -filt -first -last)
> I didn't understand what is the mathematical operation behind this
> operation
> any of you can help me?


There is a paragraph in the GROMACS reference manual which cites a paper
which uses this method. I suggest starting with that paper and looking at
the background there and the references it cites as well.

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

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