- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: David A Case <david.case.rutgers.edu>

Date: Tue, 22 Nov 2016 14:00:16 -0500

On Tue, Nov 22, 2016, The Cromicus Productions wrote:

*> I'm able to compute the principal components of a given trajectory using
*

*> PCAsuite.
*

*> http://mmb.pcb.ub.es/software/pcasuite/pcasuite.html
*

*> Then, I can convert them into pdb files and watch the motions.
*

*> PCAsuite also gives me the eigenvalues, so I know which are the most
*

*> important.
*

*>
*

*> Now, if I understand correctly, the principal components are some "chosen"
*

*> normal modes which summarize the information of the trajectory, but how do
*

*> I know which normal mode is associated to each component I get? In
*

*> particular, I would like to know what is the associated vibration frequency
*

*> of each of the components.
*

You should read about quasiharmonic analysis, which is a (trivial) variant of

PCA analysis. Might as well start here:

%A M. Karplus

%A J.N. Kushick

%T Method for estimating the configurational entropy of macromolecules

%J Macromolecules

%V 14

%P 325-332

%D 1981

Although the method is also described in lots of textbooks and review

articles. cpptraj can compute both.

Note that, speaking strictly, none of these are true "normal modes".

....dac

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Nov 22 2016 - 11:30:02 PST

Date: Tue, 22 Nov 2016 14:00:16 -0500

On Tue, Nov 22, 2016, The Cromicus Productions wrote:

You should read about quasiharmonic analysis, which is a (trivial) variant of

PCA analysis. Might as well start here:

%A M. Karplus

%A J.N. Kushick

%T Method for estimating the configurational entropy of macromolecules

%J Macromolecules

%V 14

%P 325-332

%D 1981

Although the method is also described in lots of textbooks and review

articles. cpptraj can compute both.

Note that, speaking strictly, none of these are true "normal modes".

....dac

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Tue Nov 22 2016 - 11:30:02 PST

Custom Search