[gmx-users] Re: Re: Reference structure for g_covar

[vivek modi]

Hi Tsjerk,

Thanks a lot for your reply.
But now I will ask a very naive  question.

My study involves understanding the dynamics of a group of closely related
proteins. All of them are simulated for a period of 100ns each.
I have also analyzed the RMSD using g_rms for all of them and it  becomes
very stable after 20-30ns for all the proteins.
But when I do PCA I see high cosines (~0.8) for the first PC. For all the
other PCs the cosine content is very low.

The question is  that is it appropriate to ignore the first PC and make
inference about the motion of the protein by using other PCs ?


Thanks a lot.


Regards,

-Vivek Modi

Date: Wed, 19 Oct 2011 13:58:00 +0200
> From: Tsjerk Wassenaar <tsjerkw at gmail.com>
> Subject: Re: [gmx-users] Reference structure for g_covar
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
>        <CABzE1SjU=n78nWo+o0utM7oVdWz4HbGjeyLj8x0NbweWWLzXiw at mail.gmail.com
> >
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi Vivek,
>
> I explained related matters in some detail on this list earlier, and
> would urge not to use a structure other than the average for
> determining the components.
>
> The results on the cosine contents can be illustrated as follows:
>
> I. Using average
>
> Imagine you're moving from place A to place B. The principal component
> is B-A, and the average is (A+B)/2. Your score/projection is the
> position relative to the average; negative on one side, positive on
> the other. This ends up being a straight line in one dimension, but in
> higher dimensions you'll get a nice half cosine.
>
> II. Using fixed reference
>
> Let's say your reference is A, then your component is still B-A, but
> your score/projection is now the distance from A. It starts out at
> zero and increases. In higher dimensional space, this would give a
> projection that starts out approximately linear and levels off at some
> point. These components are awkward, and very hard to interpret.
>
> Hope it helps,
>
> Tsjerk
>
>
> On Wed, Oct 19, 2011 at 10:08 AM, vivek modi <modi.vivek2009 at gmail.com>
> wrote:
> > Hi,
> >
> > I am doing Essential Dynamics on a protein (150 residues). The simulation
> is
> > 100ns long and the RMSD becomes very stable after 25ns.
> > I have gone through the mailing list archives but could not find a
> precise
> > answer to the following question.
> >
> > When I calculate the cosine content for the first PC by taking the
> average
> > structure for fitting using g_covar it gives a very high value ~.8.
> > But when I change the reference structure to the starting structure then
> I
> > get a cosine value ~.1.
> >
> > I also repeated the same by dividing my trajectory into two equal halves
> but
> > the cosine value with average structure as a reference is always very
> high
> > while it is reasonably low with starting structure taken as reference.
> >
> > My question is why the cosine content is dependent on the fitting
> > structure used in g_covar?  And, especially, which structure is
> > recommended to use in Essential Dynamics analysis ?
> >
> >
> > Any help is appreciated.
> >
> >
> > Thanks a lot.
> >
> >
> > Regards,
> >
> > Vivek Modi
> > Graduate Student,
> > IITK.
> >
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
>
>
>
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