[gmx-users] combined ED analysis

[David]

On Tue, 2004-12-14 at 17:56 +0100, vincenzo venditti wrote:

> >I don't understand what you want to do. 
> >What do you mean with "fluctuations along eigenvectors" 
> >and with "show different averaged projections"? 
> 
> > 
> 
> If I've for example for the 4 sistems under analysis differnt averaged
> projection along the second eigenvector:
> 
>                         sistem 1                  sistem 2
> sistem 3               sistem 4
> 
> vector 2             3.378                    2.547
> -3.375                  -2.540
> 
> And I've for the same sistems along the same eigenvector different
> rmsf value:
> 
>                         sistem 1                  sistem 2
> sistem 3               sistem 4
> 
> vector 2             1.2                           0.8
> 0.5                      0.3
> 
> Could I say that sistem 1 is more flexible than the other sistem along
> this direction of motion?
Yes, since the covariance analysis is done on the combined trajectories.
However you need to consider whether, say, the first 10 eigenvectors are
equally important in all simulations, by computing the projections and
the combined volume. If, e.g. in system 3 your eigen vector 11 has the
largest msf you have to reconsider your analysis.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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