cosine content of principal components

[Former user]

Hi, Does Bio3D have an easy way to calculate cosine content of pcs? Thanks in advance,

[Xinqiu Yao]

Could you describe more specifically what you mean cosine content of pcs?

[Former user]

The cosine content of the principal components is described as an indicator for predicting if a trajectory has been convergent in other words, a good indicator of bad sampling. High cosine content indicates a non-converged trajectory (For further details: Chapter 5: Normal Modes and Essential Dynamics Steven Hayward and Bert L. de Groot) Hess introduced this I guess: Hess B. Convergence of sampling in protein simulations. Phys Rev E 2002;65:0319101–03191010