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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 15 15:52:50 CET 2015

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

In short, your system is not equilibrated.



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

> 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
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

Tsjerk A. Wassenaar, Ph.D.

More information about the gromacs.org_gmx-users mailing list