[gmx-users] Fragmented backbone

[Biplab Ghosh]

Dear Gromacs users/experts

I was doing principal component analysis with a long (1000 ns) MD
trajectory.
I have seen the protein backbone continuous (not fragmented) with the
simulation time. However, the backbone is fragmented in some trajectories
corresponding to some of the eigenvectors! The Gromacs commands used are
the following:

covar   -f protein-md-center-fit.xtc -s protein-md.tpr -o eigenval.xvg -v
eigenvec.trr -xpma covara.xpm
anaeig -f protein-md-center-fit.xtc -s protein-md.tpr -v eigenvec.trr
-first 1  -last 1  -nframes 100 -extr ev1.pdb

Where, the trajectory  protein-md-center-fit.xtc is centered using   "-pbc
mol -center -ur" and rms fitted (using -fit rot+trans)
to the protein backbone atoms in the initial frame.

Please suggest how can I get rid of this fragmented backbone!

I would appreciate any suggestion on this regard.

Thanking you
Biplab.

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