[gmx-users] PCA mathematical information

[Wes Barnett]

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?
>

Emiliano,

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
http://wbarnett.us