[gmx-users] Principale component analysis , experiment and MD comparison

[Nawel Mele]

Hi all,

I would like to compare different MD trajectories with an ensemble of NMR
structures by PCA. I performed the PCA by projecting all my MD structures
and NMR ensemble onto the eigenvectors of my NMR ensemble then plot the
result.
However, I also performed PCA for each MD trajectories separately and NMR
separately and plot the result in one figure to see the difference between
the two methods and now I am confused on the process to compare different
MD with experimental data or even with a random generator.

Any ideas?

Regards

-- 

Nawel Mele, PhD Research Student

Jonathan W Essex Group, School of Chemistry

University of Southampton,  Highfield

Southampton, SO17 1BJ