[gmx-users] Reference structure for PCA.

[Tsjerk Wassenaar]

Hi,

The commands would certainly help, including the commands for getting the
reference structure. Do note that the reference is the reference for
fitting, which is 'external', i.e. provided by the user. This is not the
same as the structure used to calculate the deviations, which is the
average structure of the frames selected.

Cheers,

Tsjerk

On Sat, Feb 9, 2013 at 7:06 PM, bipin singh <bipinelmat at gmail.com> wrote:

> 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
> > IITK.
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>
> --
> *-----------------------
> Thanks and Regards,
> Bipin Singh*
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada