[gmx-users] eigenvalues and eigenvectors with g_cluster

Rebeca García Fandiño regafan at hotmail.com
Fri May 15 00:40:48 CEST 2015

Dear Gromacs users,
I am trying to analyze a trajectory into different clusters using g_cluster in Gromacs 5.0.4.

 -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.

 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,


Dr. Rebeca García 
Santiago de Compostela University

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