[gmx-users] ED analysis

[vincenzo venditti]

>From: Ruben M Buey <ruben at akilonia.cib.csic.es>
>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 17:01:44 +0200
>
>Vicenzo, how did you concatenatesd the trajectories? Did you use -settime?
>bests,
>Ruben
>
Hi Ruben,
I've used
trjcat with -settime and -cat

Thanks a lot four reply
Vincenzo


>vincenzo venditti escribió:
>
>>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 
>>trjconv.
>>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 
>>considered.
>>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?
>>
>>Thanks in advance
>>Vincenzo
>>
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>
>--
>------------------------------------------------------
>Ruben M Buey. PhD student. Lab 308
>Centro de Investigaciones Biologicas
>Consejo Superior de Investigaciones Cientificas
>Dpt. Protein Function and Structure
>C/ Ramiro de Maeztu, 9 28040  Madrid   (SPAIN)
>Phone:   34-918373112 ext 4380
>Fax:     34-915360432
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