[gmx-users] Cosine content of an eigenvector in PCA after 100ns still 0.9
m.ebert at umontreal.ca
Thu Jan 15 16:27:33 CET 2015
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?
> 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
> 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,
>> Gromacs Users mailing list
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> * 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.
> 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.
More information about the gromacs.org_gmx-users