[gmx-users] ED analysis
vincenzovenditti at hotmail.com
Thu Oct 21 17:30:50 CEST 2004
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:
>>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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