[gmx-users] principal component and essential dynamics analysis

MGiò magiofer at gmail.com
Wed Oct 19 14:07:19 CEST 2005

I am just a beginner in ED analysis, I haven't found any tutorial, but I can
suggest some very good papers:

- Hess, B., Similarities between principal components of protein dynamics
and random diffusion, Physical Review E 62(6):8438-8448 (2000)
- Hess, B., Convergence of sampling in protein simulations, Physical Review
E 65:031910 (2002)
- Kazmierkiewicz, R., et al., Essential dynamics/factor analysis for the
interpretation of molecular dynamics trajectories, Journal of Computer-Aided
Molecular Design 13:21-33 (1999).
- Arcangeli, C., et al., Molecular dynamics simulation and essential
dynamics study of mutated plastocyanin: structural, dynamical and functional
effects of a disulfide bridge insertion at the protein surface, Biophysical
Chemistry 92:183-199 (2001).

I hope this helps,


On 10/19/05, Prof. Y. U. Sasidhar <sasidhar at chem.iitb.ac.in> wrote:
> hi,
> we are interested in performing principal component and essential
> dynamics analysis of our trajectories. Is there a tutorial/ primer
> which will help us get started ? We have no previous experience
> with this kind of analysis. Any suggestion about reading material is
> also welcome.
> --
> Sasidhar
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