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

[Caterina Arcangeli]

I thank Ran and Berk for useful and critical discussion.

Caterina



> 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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-- 
Caterina Arcangeli
ENEA, Computing and Modelling Unit (CAMO)
Casaccia Research Center - Post Bag 026
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phone +39 06.3048.6898
fax   +39 06.3048.6860
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