[gmx-users] Combined essential dynamics analysis

[Ruben Martinez Buey]

Hi all,
I´m trying to compare two similar systems (one with a ligand and the other
without it). I´ve used CONCOORD for both systems. I´ve concatenated the two
individual trajectories and run g_covar over the concatenated trajectory. Only
the first 5-7 resulting combined eigenvectors are significant.
When I project the individual trajectories over these combined eigenvectors, I
get the next results:

Average projection (mean):
eigenvec 1: -0.365220            0.457450
eigenvec 2:   0.137630          -0.169460
eigenvec 3:   0.137790          -0.319940
eigenvec 4:   0.068647          -0.078291
eigenvec 5:   0.087228            0.040858

Mean square fluctations (stddev):
eigenvec 1:   6.7204                 6.7390
eigenvec 2:   3.9814                 4.2909
eigenvec 3:   3.6093                 3.6686
eigenvec 4:   2.3390                 2.2201
eigenvec 5:   1.8614                 1.8681

(Where the first column is the protein with the ligand, and the second column
is the protein without ligand)
But the extreme projections over each eigenvector (generated by g_anaeig) are
exactly the same in both cases. So, what would be the conclusion? There are no
significant differences in the essential dynamics beetwen both systems? But the
differences in the average projections are large enough to be significant,
aren´t they? And the

Thanks in advance for your kind attention,
with best wishes,
Ruben