[gmx-users] eigenvalues

[sanjay23 at iitb.ac.in]

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
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