[gmx-users] ED analysis

vincenzo venditti vincenzovenditti at hotmail.com
Thu Oct 21 16:51:10 CEST 2004

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 
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?

Thanks in advance

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