[gmx-users] Problems with g_anaeig
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
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
How it could be fixed ?
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