[gmx-users] ED analysis

Bert de Groot bgroot at gwdg.de
Thu Oct 21 17:05:15 CEST 2004

vincenzo venditti wrote:
> Hi all,
> I'm trying to carry out a combined analysis of essential dynamics of two 
> similar systems (one with a ligand and the other without it).
> I've fitted the trajectories to the same reference structure using trjconv.
> Then I've concatenated the fitted trajectories using trjcat command.
> I've constructed and diagonalized the Cá covariance matrix using g_covar 
> command and an index file in which only Cá atoms of protein reidues are 
> considered.
> I've calculated averaged values of the projections of the separate 
> trajectories onto the concatenated eigenvectors using the -proj option 
> of g_anaeig command and averaging out the projections thus obtained for 
> each eigenvector, but the results have been
> eigenvec 1:      -3.17    -1.84
> eigenvec 2:    -10.21    -9.06
> eigenvec 3:      1.96      3.70
> (Where the first column is the protein with the ligand, and the 
> secondcolumn is the protein without ligand)
> The two individual simulations have the same length.
> Why have I not obteined simmetrical results with respect to zero?

this is indeed strange. This means that the average projection averaged over
the complete, concatenated trajectory is not zero? This should usually not
happen, unless you use non-default options in g_covar for -fit and -ref, or
if you use different trajectories or reference structures for g_covar and g_anaeig.


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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