[gmx-users] Reference structure for PCA.

bipin singh bipinelmat at gmail.com
Sat Feb 9 19:06:20 CET 2013

Hi vivek,

I have few questions related to your query:

During covariance matrix calculation, g_covar by default takes average
structure of the trajectory as a reference structure then why you are
giving it average structure of your trajectory (0-100ns) manually.
Moreover without looking at your commands which you have used, it would be
difficult for anyone that why are you getting these surprising results.
On Thu, Feb 7, 2013 at 1:26 PM, vivek modi <modi.vivek2009 at gmail.com> wrote:

> 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
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Thanks and Regards,
Bipin Singh*

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