[gmx-users] ED analysis

[Bert de Groot]

Hi,
> 
> 
> 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).

Bert

____________________________________________________________________________
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
http://www.mpibpc.gwdg.de/abteilungen/073
____________________________________________________________________________