[gmx-users] eigenvalues as a function of time
L. Michel Espinoza-Fonseca
mef at ddt.biochem.umn.edu
Sat Feb 16 04:17:42 CET 2008
Hi Tsjerk,
Indeed it does make sense! Thanks for you comments.
Cheers,
Michel
PS. After all it wasn't a waste of time, isn't it? :)
On Feb 15, 2008 4:53 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> Hi Michel,
>
> Mind the eigenvectors! If you want to know how the eigenvalues
> converge, you also have to take the convergence of your eigenvectors
> into account. It may well be that for one subtrajectory one
> eigenvector is dominant, but that for a longer subtrajectory another
> is getting more important. Now, in fact any decomposition is as good
> as any other, so your best estimate for the eigenvectors to look along
> is the set obtained from the total covariance analysis. You then
> probably want to look at the convergence of the eigenvalues along
> these modes, which are basically the variances of the projections on
> these modes. In that case, you're best bet is likely to calculate the
> variances of the projections for each subtrajectory with respect to
> the corresponding average projections. The average projections all
> converge to 0, by definition and the variances will thus converge to
> the eigenvalues.
>
> O yes, this saves you quite a bit of time constructing and
> diagonalizing covariance matrices.
>
> I hope this makes sense to you :)
>
> Best,
>
> Tsjerk
>
> On Fri, Feb 15, 2008 at 7:23 AM, L. Michel Espinoza-Fonseca
>
> <mef at ddt.biochem.umn.edu> wrote:
> > Hi Tsjerk,
> >
> > You are right. I think that by either lack of caffeine or attention
> > (most probably the second one) I wrote the intervals in a wrong way. I
> > just realized it now thanks to your email. So, going back to my
> > original post, I want to obtain the eigenvalues vs time, so then I can
> > use them to calculate the entropy of a X system using the
> > quasi-harmonic approximation. What I realized (if I'm correct this
> > time) is that I need to calculate the covariance matrix *not* from
> > isolated intervals (such as 0-500, 501-1000, etc.) but from intervals
> > starting from the reference structure (0-500, 0-1000, 0-1500, etc.).
> > The goal is simply to determine to what extend the entropy converges
> > in the simulation, as it has been shown that relatively long
> > simulations are needed for this term to converge.
> >
> > On the other hand, splitting wasn't the right word, after all. Even
> > now I can't find the right word. I slipped up twice.
> >
> > I apologize for my mistake -I basically took from you a few minutes
> > because of my lack of clarity :)
> >
> > Cheers,
> > Michel
> >
> >
> >
> > On Thu, Feb 14, 2008 at 11:47 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> > > Hi Michel,
> > >
> > > You're principal components will be heavily undersampled (and
> > > therefore underdetermined), most notably the higher ones. You're
> > > likely not even to have more than a single uncorrelated observation
> > > per subtrajectory. The eigenvalue is a measure of the fluctuation, or
> > > actually the spread, over time. It's not that trivial to split that.
> > > Also note that we usually neglect the fact that we have too few
> > > independent observations in a trajectory as it is. You're just making
> > > things worse.
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > >
> > >
> > > On Thu, Feb 14, 2008 at 11:33 PM, L. Michel Espinoza-Fonseca
> > > <mef at ddt.biochem.umn.edu> wrote:
> > > > Mark,
> > > >
> > > > I have one more question. For example, if I have a trajectory of 10 ns
> > > > divided in intervals of 10 ps each, to obtain a set of eigenvalues
> > > > each 500 ps I have to calculate the eigenvalues using the following
> > > > intervals:
> > > >
> > > > 0-500 ps
> > > > 501-1000 ps
> > > > 1001-1500 ps
> > > > ....
> > > > 9501-10000 ps
> > > >
> > > > Is that correct?
> > > >
> > > > Thanks!
> > > >
> > > > Michel
> > > >
> > > > On Thu, Feb 14, 2008 at 2:54 AM, Marcus Kubitzki <mkubitz at gwdg.de> wrote:
> > > >
> > > >
> > > > > Hi Michel,
> > > > >
> > > > > I'm confused by what you mean by "splitting" the eigenvalues.
> > > > > With g_covar -b -e you can get eigenvals for a specified interval of
> > > > > time, e.g. 0-1ns. Getting eigenvals as a function of time (if that's
> > > > > what I suspect you want to do), you need to run g_covar for all
> > > > > intervals 0-t1, 0-t2, 0-t3, ... to get the desired sequence.
> > > > >
> > > > > Marcus
> > > > >
> > > > >
> > > > >
> > > > >
> > > > > L. Michel Espinoza-Fonseca wrote:
> > > > > > Hi all,
> > > > > >
> > > > > > I have a MD trajectory and want to split the eigenvalues as a function
> > > > > > of time. I've been trying to do so with g_covar but with no success.
> > > > > > I'd like to know if you could guide me on this matter. I'm planning to
> > > > > > further used those values to calculate the entropy (By using Karplus'
> > > > > > approximation) vs time and its convergence in the simulation.
> > > > > >
> > > > > > Cheers,
> > > > > > Michel
> > > > > > _______________________________________________
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> > > > > --
> > > > > Marcus Kubitzki
> > > > > Max Planck Institute for Biophysical Chemistry
> > > > > Computational Biomolecular Dynamics Group
> > > > > Am Fassberg 11
> > > > > D-37077 Göttingen
> > > > > Germany
> > > > > phone: ++49-551-2012312
> > > > > fax: ++49-551-2012302
> > > > > Email: mkubitz[at]gwdg.de
> > > > > www: http://www.mpibpc.mpg.de/groups/de_groot/
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> > >
> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
> > > Junior UD (post-doc)
> > > Biomolecular NMR, Bijvoet Center
> > > Utrecht University
> > > Padualaan 8
> > > 3584 CH Utrecht
> > > The Netherlands
> > > P: +31-30-2539931
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> > >
> > >
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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