[gmx-users] COMB ED

Ruben Martinez Buey ruben at akilonia.cib.csic.es
Tue May 6 17:41:02 CEST 2003

Dear Gromacs users,
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:

I´m trying to do an ED analysis on two different MD simulations; GDP and GTP
conformations of the same protein.
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.
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,
how can I see the average projections of the MD simulation time frames of the
separate gtp and gdp MD trajectories onto the eigenvectors calculated from the
combined trajectory?
And the mean square fluctuations in the projection?
Can I do it with g_anaeig in GROMACS?

Thanks a lot in advance for your kind atention,
with best wishes,

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