[gmx-users] Re: questions about Principal Component Analysis

Thomas Evangelidis tevang3 at gmail.com
Sun Apr 8 21:43:13 CEST 2012

Hi Tsjerk,

Thank you for all the clarifications. Just one more thing, I excluded the
loop residues with RMSF>4 A. (because their movement is dominated by random
diffusion), did PCA on the rest of the protein, and the cosine content
improved significantly. Is this procedure acceptable?

Thanks in advance.

On 6 April 2012 00:12, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Thomas,
> First of all, proteins in solution don't suddenly stop with Brownian
> motion at some point. It's just the way things move at the microscopic
> level. Second, the cosine content has nothing to do with randomness.
> Really. Nothing. On the contrary. The cosine content indicates
> unidirectional motion. I repeat, the cosine content has NOTHING to do
> with RANDOM motion! Really really. High cosine content?
> U-ni-di-rec-tio-nal motion; movement from one point to another point.
> The trick is realizing that the best reaction coordinate for random
> motion from point A to point B is the straight line between A and B.
> Unfortunately, the RMSIP is no help where it comes to convergence. It
> only tells you whether the directions in conformational space along
> which most of the motion takes place is similar between two (parts of)
> simulations. For convergence, you want to check the projections, and
> the cosine content thereof. The cosine content should indeed be low.
> Your case, with relatively high cosine content in every window,
> suggests that there is still motion, c.q. conformational
> rearrangement, on route to another state of the system. I fear there
> is no other way of looking at it that will suggest it has converged
> already. Actually, 20 ns is very little for equilibration, especially
> if convergence requires rearrangement of protein-protein interactions.
> Cheers,
> Tsjerk


Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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