[gmx-users] PCA analysis results

Nithyanan Annamalai nithyanny90 at gmail.com
Fri Dec 18 20:34:52 CET 2015

Dear GROMACS users,

I have performed 50ns MD for 567 aa monomer protein using gromos53a6 ff in
explicit water in the cubic box with 2fs time step.

I have  used g_covar and g_anaeig to perform Principal Component Analysis/
Essential Dynamics analysis.

But when I view the animation of the trajectory it, the movement of the
protein looks weird.

Can anyone please help to explain to me what I can do to get the right

Link for eigenvalue file:


I have used the following command line to extract the results:

g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v
../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig
../../phac_monomer_50ns_wild_Protein_eigenval.xvg -filt mono_wild_filt1.pdb
-rmsf mono_wild_PC1_eigrmsf.xvg -first 1 -last 1 -skip 100

pdb file link:


 g_anaeig -f ../../md_0_1.xtc -s ../../md_0_1.tpr -n ../../index.ndx -v
../../phac_monomer_50ns_wild_Protein_eigenvec.trr -eig
../../phac_monomer_50ns_wild_Protein_eigenval.xvg -extr
mono_wild_extreme1.pdb  -first 1 -last 1 -nframes 50

pdb file link:

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