[gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9

Ebert Maximilian m.ebert at umontreal.ca
Thu Jan 15 15:43:43 CET 2015

Hi there,

I have one question regarding the cosine content of an eigenvector. I did a PCA and calculated the cosine content of the 10 main eigenvectors. Except for the first all are really low. However, the main eigenvector is still around 0.9 after 100ns simulation. I am pretty sure my system is equilibrated. Do you have any idea what might happen?

Thank you very much,


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