Hi Ibrahim
>> I can not understand which are the eigenvectors and eigenvalues in the
file.
Here they are: Just see **** in your file and further explanation here
http://archive.ambermd.org/201209/0153.html
If am not wrong Variance corresponds to the Eigenvalue (someone can chime
in!). You can read something here:
"The eigenvalues in PCA tell you how much variance can be explained by its
associated eigenvector" (
http://stats.stackexchange.com/questions/31908/what-is-percentage-of-variance-in-pca
)
>> Porcupine Plot from this evecs file
You can have Porcupine ploting script tar file from here:
http://archive.ambermd.org/201211/0411.html
regards
On Fri, May 9, 2014 at 5:58 PM, Ibrahim Said <saidibrahim569.gmail.com>wrote:
> Dear Amber users
> I have an evecs.dat file extracted from the molecular dynamics of 5-ns for
> my protein using Amber12. unfortunately, I can not understand which are the
> eigenvectors and eigenvalues in the file. Please can someone guides me to
> calculate both cumulative variance and Porcupine Plot from this evecs file.
> I attached a part of this evecs.dat file
>
> Kind Regards,
>
> said
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 09 2014 - 11:00:02 PDT
