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

[Thomas Evangelidis]

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.
Thomas



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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