[gmx-users] ED analysis

Bert de Groot bgroot at gwdg.de
Thu Oct 21 18:42:32 CEST 2004

> No. For G_covar I've used concatenated_trajectory.xtc (obteined from 
> trjcat between protein-substrate trajectory and protein trajectory), 
> instead for g_anaeig I've used separate trajectories.

OK, then the first check should be to run g_anaeig -proj using the
concatenated trajectory and compare the projections to those of the
two individual trajctories. (and to check if the average projection
over the concatenated trajectory *is* zero, as it should be by definition).

> I've carried out two MD simulations (1 ns) on the two sistems.
> Then I've fitted the two trajectories at the same tpr file using -fit 
> option of trjconv command.
> I've concatenated the two trajectories using trjcat with -settime and -cat.
> I've costructed and diagonalized the covariance matrix using g_covar 
> command with -mwa, -f the concatenated trajectories, -s the same tpr 
> file included in trjconv, -n an index file in which only protein Ca have 
> been considered.
> I've computed the projection of the separate trajectories onto the 
> concatenated eigenvectors by the use of
> g_anaeig -v concatenated_eigenvectors.trr -f protein_trajectory.xtc (and 
> then protein-substrate_trajectory.xtc) -s file.tpr (the same of trjconv 
> and g_covar) -n file.ndx (the same of g_covar) -proj output.xvg

the procedure looks fine (although I don't see the need for an index file as
the Ca's are a standard group in gromacs). So, again, if you can't find the
error: send me (ie not the list) a minimal set of files with which the
problem can be reproduced).


Dr. Bert de Groot

Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
37077 Goettingen, Germany

tel: +49-551-2012308, fax: +49-551-2012302

email: bgroot at gwdg.de

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