[gmx-users] questions about Principal Component Analysis

Thomas Evangelidis tevang3 at gmail.com
Wed Mar 7 20:56:26 CET 2012

Dear GROMACS community,

I have two questions regarding PCA. I have run MD simulations for 70 ns for
a protein of 1100 amino acids, of which I decided - based on the RMSD - to
analyze the last 50.

1) The protein consists of 5 domains, out of which only one is of interest
in this study. Is it right to do draw conclusion from PCA restricted that
domain (400 aa)?

2) How can I find out if the simulation time is sufficient to do PCA?

Thanks in advance for any feedback.




Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

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