[gmx-users] ED analysis

vincenzo venditti vincenzovenditti at hotmail.com
Thu Oct 21 18:16:54 CEST 2004

>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 

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

>(or 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
>gmx-users mailing list
>gmx-users at gromacs.org
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