[gmx-users] ED analysis: help on cosine content and overlap ofthe fluctuatio

[Berk Hess]

I agree with Ran.

But on your quesion of inconsistency.
It seems like your essential subspace (the space spanned by
the first 10 eigenvectors) has converged.
But this does not say much about the convergence of the
first few eigenvectors in this subspace.
>From the cosine content one can clearly say that M1 is not
converged. Since M2 is a subset of M1 it is also not converged.
So for proper sampling of global conformations you would need
to simulate several orders of magnitude longer,
as one would expect for a 253 residue protein.
If you need this for what you are interested in is another question.

Berk.


>From: Ran Friedman <r.friedman at bioc.unizh.ch>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] ED analysis: help on cosine content and overlap 
>ofthe	fluctuations
>Date: Fri, 13 Apr 2007 13:44:19 +0200
>
>Dear Caterina, GMX users,
>
>It's very difficult to decide whether a simulation converged, at least
>for macromolecules. There are a lot of studies in the literature about
>it, but there's no concrete answer. I'd try to ask when the results can
>be useful, and not when the simulation (or PC) converged - and that
>depends on your system and what you are trying to model. One hint is
>that a PC with a high cosine content is probably not going to be very
>useful if you try to simulate any kind of structural transitions.
>
>Ran.
>
>Caterina Arcangeli wrote:
> > Dear all,
> >
> > I performed essential dynamics (ED) analysis on my protein (253 amino
> > acids). The simulation (10ns) achieves stability in the RMSD after
> > 6.0ns, but a convergence analysis based on cluster analysis (as
> > described by Daura, 1999) indicates that the conformational sampling
> > reaches a stable value only for the last 1.0ns.
> >
> > So, I've performed ED on both 6-10 ns (M1) and 9-10ns (M2) time interval
> > using g_covar.
> >
> > To check if the principal modes are well defined, I've calulated the
> > ovelap of the sampling between the first and second half of the
> > trajectories (I've splitted M1 and M2 into two halves) and the cosine
> > content of the first eigenvectors:
> > - the normalized overlaps are 0.499 (M1) and 0.434 (M2);
> > - the subspace overlaps (rmsip) for the first 10 eigenvectors are 0.748
> > (M1) and 0.686 (M2);
> > - the cosine content of the first eigenvectors is 0.828 (pc1) for M1 and
> > 0.125 (pc1) for M2.
> >
> > So, apparently, the two method are inconsistent:
> > a higher rmsip value is observed for M1 (according to Amadei, a rmsip
> > value > 0.7 shows a reasonable convergence) wheras the lower cosine
> > content is obtained for M2 (according to Hess, a value < 0.5 indicates
> > jumping between clusters and not a merely random diffusion).
> >
> > My questions are: which time window better describe the dynamics of my
> > protein? From where come out this inconsistency? What I'm wrong?
> > Thank to all.
> >
> > Caterina
> >
> >
> >
> >
> >
> > P.S. I aware that 10 ns are in general insufficient to describe the
> > thermodynamics of a protein but I want just to have an idea of some
> > structural properties of my protein.
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
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> >
> >
>
>
>--
>------------------------------------------------------
>Ran Friedman
>Postdoctoral Fellow
>Computational Structural Biology Group (A. Caflisch)
>Department of Biochemistry
>University of Zurich
>Winterthurerstrasse 190
>CH-8057 Zurich, Switzerland
>Tel. +41-44-6355593
>Email: r.friedman at bioc.unizh.ch
>Skype: ran.friedman
>------------------------------------------------------
>
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