[gmx-users] COMB ED

Bert de Groot bgroot at gwdg.de
Tue May 6 17:46:01 CEST 2003

Ruben Martinez Buey wrote:
> 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?

if you already have projections of each part separately, then you can
simply read the average+standard deviations in xmgr under 'data->status'
(in xmgrace it's slightly more hidden).



Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Theoretical molecular biophysics group
Am Fassberg 11 
37077 Goettingen, Germany

tel: +49-551-2011306, fax: +49-551-2011089

email: bgroot at gwdg.de

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