[gmx-users] ED analysis

Ruben M Buey ruben at akilonia.cib.csic.es
Thu Oct 21 17:01:44 CEST 2004

Vicenzo, how did you concatenatesd the trajectories? Did you use -settime?

vincenzo venditti escribió:

> 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?
> Thanks in advance
> Vincenzo
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Ruben M Buey. PhD student. Lab 308
Centro de Investigaciones Biologicas
Consejo Superior de Investigaciones Cientificas
Dpt. Protein Function and Structure
C/ Ramiro de Maeztu, 9 
28040  Madrid   (SPAIN)
Phone:   34-918373112 ext 4380
Fax:     34-915360432

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