[gmx-users] ED analysis

[vincenzo venditti]

>From: Bert de Groot <bgroot at gwdg.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] ED analysis
>Date: Thu, 21 Oct 2004 17:45:02 +0200
>
>vincenzo venditti wrote:
>>
>>Hi Bert,
>>I've used g_covar with default options and I've used the same tpr file for 
>>g_covar and g_anaeig.
>
>and also the same .xtc (or .trr) file?

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.

>
>>Perhaps have I to use the average.pdb file (obtained with -av option of 
>>g_covar command) as reference structure for g_anaeig command?
>
>no, g_covar stores the average (and reference) used during the covariance 
>analysis in the
>eigenvec.trr file, so this should automatically be correct.
>
>If you can't find the mistake, please specify step by step what you've 
>done.

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

Thanks for your help
Vincenazo



>(or 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
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