[gmx-users] Reference structure for PCA.

[vivek modi]

Hello,

I have troubled you with a similar question before also, but I guess I need
some more clarification. My question is about the reference structure in
PCA analysis.
I have 100ns long protein simulation which I want to analyze using PCA. The
RMSD shows fluctuations upto initial 25-30ns and then becomes very stable.
I have performed PCA on the last 30ns window of the simulation where I
assume the simulation has converged (I also did on other time windows as
well).

The question is this:
I did the analysis on the last 30ns window in two ways by taking two
different reference structures.

a. I take the average structure of the trajectory (0-100ns) as
the reference and then do the fitting and calculate covariance matrix for
last 30ns. This is done because I suspect that the average structure over
full trajectory will reflect all the changes occurring in the protein. It
also gives me low cosines (<0.1). The PCs show movement occurring in
certain regions of the protein.

b. I take the average structure from the same window (last 30ns) then do
the fitting and calculate covariance matrix for the same. This is done with
an assumption that the reference structure must reflect the
equilibriated/stable part of the trajectory unlike the previous case.
Surprisingly it gives me high cosines (>0.5). Unlike the previous case,
this method shows very small movement in the protein (very low RMSF).

Both of these methods give me different RMSF for the PCs although they are
done on the same part of the trajectory but the reference structure is
influencing the output.

 Which protocol among the two is appropriate ?  And how can we explain high
cosines in second case where the reference structure is the average of the
same time window (there must not be large deviation) while I get low cosine
for the first case where deviations are calculated from the full trajectory
average (large deviation) ?

Any help is appreciated.

Thanks,

-Vivek Modi
Graduate Student
IITK.