[gmx-users] Problems with g_anaeig

Mark Abraham mark.j.abraham at gmail.com
Thu Jan 24 21:37:26 CET 2013

On Tue, Jan 22, 2013 at 8:22 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Dear Gromacs users!
> There is some bug  with g_anaeig the souce of which I could not fully
> understand.

Good Advice: until you can almost write a code patch to fix it, be very
hesitant in suggesting any software has a bug. The best people to help
solve the issue are often those who wrote the code, and you don't want them
annoyed with you :-)

  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 ?

How have you excluded the hypotheses that your reference structure is not a
valid representative of the middle of the range of variation? Or even that
the X-ray structural ensemble really is one?


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