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

Thomas Evangelidis tevang3 at gmail.com
Thu Apr 5 14:38:50 CEST 2012

Dear Tserk and the rest of GROMACS users,

Last time I measured the cosine content of different time intervals from
the PCs of the whole trajectory. This time I did PCA for each time interval
and measured the cc which is the right way I suppose. Maisuradze et al.,
2009 claim that a CC value below 0.5 indicates that the protein-water
system stops behaving as one with Brownian motions. Yet in none of my time
intervals the CC dropped below 0.6. Can this happen for an equilibrated

It is known that RMSIP can be used to measure the overlap between essential
subspaces. My question is can RMSIP
help me decide at which point to consider a system equilibrated from a
thermodynamical point of view, namely the point at which the system stops
doing Brownian motion? Does this point necessarily coincide with that where
the RMSD is stabilized?

Our protein is co-complexed in another one in the crystal structure, which
is believed to hold it in an "inactive state". However, we simulate the
monomer state, hence we expect a large domain motion to occur in the first
few nanosecond. Provided that the first 20ns are considered the time for
equilibration, does it make sense to do PCA in this time interval?

Thanks in advance for your help.


On 12 March 2012 15:44, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Thomas,
> Whether or not it makes sense to do PCA on the domain only depends on
> the question you ask. It may well make sense if you aim at
> characterizing the intra-domain motions. But be aware that you will
> view those motions within the context of the rest of the protein. It
> is quite likely that the internal motions depend on the interaction
> with the surroundings.
> Concerning the cosine content, there indeed seems to ba a transition.
> But that is already evident from your RMSD plot. A lot of stuff is
> still happening in the second half of the simulation. To see if the
> last part of your simulation is in a (local) equilibrium, you can
> calculate the average structure from that part, say the alst 10 or 20
> ns, and determine the RMSD against the average. The RMSD should then
> decrease towards the average and level off or oscillate around it to
> assure you've reached some sort of equilibrium. On the basis of that
> you could then decide whether it's worthwhile performing PCA on that
> part only.
> 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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