[gmx-users] Fragmented backbone

Tsjerk Wassenaar tsjerkw at gmail.com
Fri Feb 19 09:17:57 CET 2016

Hi Biplab,

There are different ways of being fragmented and it may be helpful to post
alink to an image. But as a general note, the filtered/extreme structures
are hardly ever physical.



On Fri, Feb 19, 2016 at 5:17 AM, Biplab Ghosh <ghosh.biplab at gmail.com>

> 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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Tsjerk A. Wassenaar, Ph.D.

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