[gmx-users] PCA comparison between two simulations

Thomas Evangelidis tevang3 at gmail.com
Sun Sep 23 18:17:09 CEST 2012


I would first do an alignment between the two proteins and then do PCA
using only the Ca atom coordinates of the common atoms (or the ones you
think are equivalent). I would also remove the very flexible loops to
extract pure low-frequency motions with PCA. At the end you must have two
eigenspaces that correspond to the same number of Ca atoms, which you can
compare using the Root Mean Square Inner Product of selected PCs. For
example, to measure the inner productions between eigenvectors 1-3 you can

g_anaeig -v eigenvec1.trr -eig eigenval1.xvg -v2 eigenvec2.trr -eig2
eigenval2.xvg -inpr -first 1 -last 3

There are a few more option of g_anaeig you can experiment with.


On 23 September 2012 18:25, francesco oteri <francesco.oteri at gmail.com>wrote:

> Dear gromacs users,
> I've simulated two different proteins (different atom number) and I carried
> out the pca analysis
> for the two simulations. Now I'd like to know whether there is a similarity
> between the eigenvectors
> of the two simulation, i.e. whether the 1st eigenvector of simulation1 is
> similar to the 3rd eigenvector
> of simulation2. In my case, the eigenvector direction is enough as
> definition of similarity.
> Can you help me? please
> Francesco
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Thomas Evangelidis

PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens

email: tevang at pharm.uoa.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/

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