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Dear Gromacs users,
<br>I would like to make you some questions about COMB-ED analysis, referring
to the several papers by Dr. van Aalten and/or Dr. de Groot:
<p>I´m trying to do an ED analysis on two different MD simulations;
GDP and GTP conformations of the same protein.
<br>The GDP bound structure is in the PDB and this is the starting structure.
Further, gamma phosphate atoms are added to GDP for the GTP simulation.
<br>Both simulations are run with the same parameters using GROMOS96. I
am trying to do the ED analysis with GROMACS v 3.1.4, but I don´t
know how to compare the two trajectories. I´ve constructed a combined
trajectory by concatenating the last 300 psec of each gdp and gtp trajectories.
I´ve constructed a covariance matrix and diagonalized it, resulting
the "combined eigenvectors" (using g_covar in GROMACS). I can project now
the two separate trajectories onto the comb eigenvectors, but,
<br>how can I see the <u>average projections</u> of the MD simulation time
frames of the separate gtp and gdp MD trajectories onto the eigenvectors
calculated from the combined trajectory?
<br>And the <u>mean square fluctuations</u> in the projection?
<br>Can I do it with g_anaeig in GROMACS?
<p>Thanks a lot in advance for your kind atention,
<br>with best wishes,
<br>Ruben
<br>
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