Dear Gromacs users,
I am trying to analyze a trajectory into different clusters using g_cluster in
Gromacs 5.0.4.
g_cluster
-f trajectory_fit.xtc -s minimizado.tpr -g clusters_300K_vac.log -cl
clusters_300K_vac.pdb -cutoff .1 -dist rmsd-dist300.xvg -o
rmsd-clust_300.xpm -sz clust-size_vac.xvg -ev rmsd-eig.xvg -method
diagonalization -n index_noH.ndx
In the documentation, the option -ev is described as:
-ev writes the eigenvectors of the RMSD matrix diagonalization.
However,
the output rmsd-eig.xvg does not represent the eigenvectors, but the
eigenvalues. The x coordinates are the number of structures to analyze
in the cluster analysis.
@ title "RMSD matrix Eigenvalues"
@ xaxis label "Eigenvector index"
@ yaxis label "Eigenvalues (nm\S2\N)"
@TYPE xy
0 -55.6214
1 -40.9801
2 -19.5495
3 -16.792
(...)
Is there any way to calculate the eigenvectors of the RMSD matrix?
Thanks a lot for your help in advance.
Best wishes,
Rebeca.
Dr. Rebeca García
Santiago de Compostela University
Spain
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