[gmx-users] PCA with Gromacs

[zeineb SI CHAIB]

Dear Gmx users,

I've been using Gromacs to perform Principal Component Analysis on my trajectories.

1- With gmx anaeig, we can plot a 2d projection of a trajectory on eigenvectors 1 and 2 (for example). I would like to know if there is a way to obtain the same plot but where the points are color-coded according to MD time?

2-I also would like to know how the diagonalization of the covariance-matrix with gmx covar is done: Is it by Eigenvalue decomposition (EVD) or Singular value decomposition (SVD)? I couldn't find the information on the manual...

Thank you in advance for your help.

Zeineb