[gmx-users] Problems with g_anaeig

James Starlight jmsstarlight at gmail.com
Tue Jan 22 20:22:32 CET 2013

Dear Gromacs users!

There is some bug  with g_anaeig the souce of which I could not fully
understand.   I have problems when I perform PCA of X-ray data set.
Below you can my workflow.

g_covar -f b2ar_xray_coors.pdb  -s ref.pdb  -o PCA_eigenval.xvg -v
PCA_eigenvec.trr -av PCA_average.pdb -last 8
g_anaeig -v PCA_eigenvec.trr -s ref.pdb  -f b2ar_xray_coors.pdb -rmsf
eigrmsfPCA.xvg -filt

here b2ar_xray_coors.pdb  is the trajectory made from 10 X-ray
structures of my protein (only main chain atoms are included)
ref_pdb is the first frame of that trajectory

As the result I've obtained reasonable eigenvalues and aigenvectors
from g_covar BUT when I check filter trajectory ( produced by
g_anaeig) fitted it to the ref.pdb or to the averaged structure in
both cases I've obtained very distorted geometry of the  protein in
thefiltered trajectory. I have no such problems in case of PCA of MD
trajectory ( when  -f trajectory.trr is from the md snapshots not from
x-ray structures)

How it could be fixed ?


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