[gmx-users] Re: gmx-users Digest, Vol 106, Issue 52

[Tsjerk Wassenaar]

Don't use the option -ref. I've explained the how and why extensively some
while ago.

Cheers,

Tsjerk


On Sun, Feb 10, 2013 at 11:26 AM, vivek modi <modi.vivek2009 at gmail.com>wrote:

> > Message: 2
> > Date: Sat, 9 Feb 2013 23:36:20 +0530
> > From: bipin singh <bipinelmat at gmail.com>
> > Subject: Re: [gmx-users] Reference structure for PCA.
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID:
> >         <
> > CAKb2Z-FU2qepKhOHfJE5RJ7Sk80DU8cSSzuQQCn-jgdpvbvpnQ at mail.gmail.com>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > 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.
> >
>
> Thank you Bipin for your reply.
> I am doing this because I have found that the result of the analysis
> changes with the reference structure. And if my understating is correct
> then g_covar by default does not take the complete trajectory structure as
> the reference; it takes the average structure of the time window on which
> we perform the analysis. Following are the commands which I am using for
> g_covar:
>
> 1. g_covar  -f  *.xtc  -s  average0-100ns.pdb  -o  -v   -n  -b  70000  -e
>  100000  -av  xyz.pdb  -l  xyz.log  -ascii  xyz.dat  -xpm  xyz.xpm  -mwa
>  -ref (trajectory average is the reference)
>
> 2. g_covar  -f  *.xtc  -s  average70-100ns.pdb  -o  -v   -n  -b  70000  -e
>  100000  -av  xyz.pdb  -l  xyz.log  -ascii  xyz.dat  -xpm  xyz.xpm  -mwa
>  -ref
> (70-100ns average is the reference)
>
> Method 1 gives me low cosines (<.1).
> Method 2 gives high cosines (~.5-.6) which I can not understand why. Also
> the RMSF which these methods report are different.
> Which reference structure is then appropriate and why ?
>
>
> Thanks and Regards,
>
> -Vivek.
>
>
> 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