[gmx-users] eigenvalues

[Xavier Periole]

On Thu, 8 Jan 2009 16:31:01 +0530 (IST)
  sanjay23 at iitb.ac.in wrote:
> dear gromacs users,
> 
> i did PCA analysis for my trajectory using g_covar and g_anaeig, i have
> taken trajectory of 25ns from both protein alone and protein_withligands(i
> did two simulation one with ligands and other by removing the ligands from
> pdb file)and extracted eigenvalues along first 10 eigenvector, when i
> compared eigenvalues i find that protein_withligands has high values in
> compare to protein alone,  but from literature protein alone is more
> flexible structure and after ligand binding it changes in to more rigid
> structure. primary analysis like RMSD, RMSF calculation showing high
> values for protein alone in compare to protien_withligands. i think i
> should also get higher eigenvalue for protein alone.. is any thing wrong
> with my trajectory. i had used same mdp file for both simulation. i am
> sending values of Ist 10 eigenvector for make my question more clear. any
> suggestion is appreciable
The eigenvalues alone do not mean much. They probably do not correspond to
the same eigenvectors. You have to compare the eigenvectors from the two
simulations. This is possible using a RMSIP (root mean square inner product).
You'll find the definition and more details in papers from Amadei and Ceruso.
hints: Amadei et al., 1999; Ceruso et al., 1999a,b, 2003; Merlino et al., 
2003; Roccatano et al., 2003

Best,
XAvier.
> protein-withligands
> 1 1.48497
> 2 0.674994
> 3 0.410547
> 4 0.279636
> 5 0.237182
> 6 0.213209
> 7 0.158359
> 8 0.140052
> 9 0.126227
> 10 0.113618
> 
> protein alone
> 1 0.526848
> 2 0.351471
> 3 0.267247
> 4 0.248945
> 5 0.222829
> 6 0.204475
> 7 0.158441
> 8 0.12583
> 9 0.0970591
> 10 0.0923962
> 
> 
> 
> thanks
> sanjay
> 
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-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
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