[gmx-users] eigenvalues as a function of time

[Tsjerk Wassenaar]

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
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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