Date: Tue, 6 Feb 2018 15:50:52 +0100
Dear Amber users,
I have performed simulations on a small peptide (18 residues). I performed
dihedral PCA on the results and analyzed correlation matrices to find out
correlated motions amongst various sections of the peptide. I read the
previous answers about the differences in PCA and quasi-harmonic analysis.
Is it more beneficial to carry out quasi-harmonic analysis for such
motions? I don't really understand the idea behind it but I performed the
calculation. The matrix 'mwcvmat.dat' when plotted as a heatmap doesn't
show anything interesting in comparison to dihedral PCA matrices.
Also the file 'thermo.dat' with thermo chemistry calculation and the first
20 modes is produced. I am unable to apply the information to my simulation
results. Does it show stability in simulation? What does the various energy
terms calculated for each mode signify?
I am attaching the heatmap of the matrix.
[image: Inline image 1]
Any help or advice is appreciated.
-- Best wishes Chetna
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