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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 20 18:22:53 CEST 2011

Hi Vivek,

The high cosine content of the first pc indicates that the system is still
equilibrating. You're sort of still on the road from A (the starting
position) to B (the equilibrated state).

Hope it helps,


On Oct 20, 2011 5:07 PM, "vivek modi" <modi.vivek2009 at gmail.com> wrote:

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.


-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...

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