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

[Ebert Maximilian]

Hi Tsjerk,

thanks for your reply. Can you explain this sentence again please:

Not having a full set of cosines with periods equal to half the pc index just means you're not simulating gas or liquid.

The simulation runs already for 500ns and I analyzed 100ns from 400 to 500ns. How can a simple protein system not be equilibrated yet?

Max

> On Jan 15, 2015, at 3:52 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 
> 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.
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