AMBER Archive (2009)

Subject: RE: [AMBER] PCA analysis with ptraj

• Previous message: Oliver Kuhn: "[AMBER] three trials to create topologies with sleap and tleap"
• In reply to: hannes.loeffler_at_stfc.ac.uk: "RE: [AMBER] PCA analysis with ptraj"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

Thank you, that's what I did but I wasn't sure about the "correctness"
of the operation.

Thanks again, best regards

Alessandro

Il giorno mar, 10/11/2009 alle 08.13 +0000, hannes.loeffler_at_stfc.ac.uk
ha scritto:
> > However, I didn't found a tool or a command to
> > allow the calculation of the contribution of each eigenvector to the
> > total motion of my system.
>
> You simply compare the eigenvalue (=variance along the correpsonding mode)
> of interest with the sum of all eigenvalues (you can get the same value
> from the sum of diagonal elements of the matrix).
>
>
> > (i.e. I don't see 3N rows and 3N lines).
>
> Well, it might not be stored in that way but if you sum up all entries you
> will arrive at 3N X 3N.
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

• Previous message: Oliver Kuhn: "[AMBER] three trials to create topologies with sleap and tleap"
• In reply to: hannes.loeffler_at_stfc.ac.uk: "RE: [AMBER] PCA analysis with ptraj"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]