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

[Tsjerk Wassenaar]

Hi Max,

The cosine content is a rather nonsensical parameter.
HOWEVER, having a cosine content with 1/2 period that high one ANY
eigenvector is indicative of unidirectional motion (a.k.a. conformational
change/drift). That cosine contents with other periods on other
eigenvectors is low is meaningless. Not having a full set of cosines with
periods equal to half the pc index just means you're not simulating gas or
liquid.

In short, your system is not equilibrated.

Cheers,

Tsjerk

On Thu, Jan 15, 2015 at 3:43 PM, Ebert Maximilian <m.ebert at umontreal.ca>
wrote:

> 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,
>
> Max
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-- 
Tsjerk A. Wassenaar, Ph.D.