[gmx-users] ED analysis

vincenzo venditti vincenzovenditti at hotmail.com
Thu Oct 21 17:30:50 CEST 2004

Hi Bert,
I've used g_covar with default options and I've used the same tpr file for 
g_covar and g_anaeig.
Perhaps have I to use the average.pdb file (obtained with -av option of 
g_covar command) as reference structure for g_anaeig command?
Thanks a lot four reply

>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 17:05:15 +0200
>vincenzo venditti wrote:
>>Hi all,
>>I'm trying to carry out a combined analysis of essential dynamics of two 
>>similar systems (one with a ligand and the other without it).
>>I've fitted the trajectories to the same reference structure using 
>>Then I've concatenated the fitted trajectories using trjcat command.
>>I've constructed and diagonalized the Cá covariance matrix using g_covar 
>>command and an index file in which only Cá atoms of protein reidues are 
>>I've calculated averaged values of the projections of the separate 
>>trajectories onto the concatenated eigenvectors using the -proj option of 
>>g_anaeig command and averaging out the projections thus obtained for each 
>>eigenvector, but the results have been
>>eigenvec 1:      -3.17    -1.84
>>eigenvec 2:    -10.21    -9.06
>>eigenvec 3:      1.96      3.70
>>(Where the first column is the protein with the ligand, and the 
>>secondcolumn is the protein without ligand)
>>The two individual simulations have the same length.
>>Why have I not obteined simmetrical results with respect to zero?
>this is indeed strange. This means that the average projection averaged 
>the complete, concatenated trajectory is not zero? This should usually not
>happen, unless you use non-default options in g_covar for -fit and -ref, or
>if you use different trajectories or reference structures for g_covar and 
>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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