[gmx-users] g_rms , getting rmsd matrix and the histogram of this matrix

[Xavier Periole]

On Tue, 12 Feb 2008 20:56:04 +0200
  "OZGE ENGIN" <OZENGIN at KU.EDU.TR> wrote:
> Hi all, 
> 
> I have three questions. 
> 
> 1)In order to get the rmsd distribution of all the conformations, I used 
>g_rmsd. In the help menu, it is stated that g_rmsd compares the structure 
>given by -s and compares it to the others which are given by -f option. 
>Consequently, I can not get the rmsd between all pairs of conformations. how 
>can I get the rmsd between all of the pairs?

g_cluster can give you the distribution of the pairwise rmsd. I guess that
is what you are looking for.

> 2)How can I get the rmsd matrix? In manual, it is indicated that with option 
>-m, you produce a matrix. However, with xv, I can not see the matrix exactly. 
> 3)Is there any specific tool for plotting the histogram of the rmsd matrix?

g_cluster

> 
> Thanks in advance
> 
> Ozge Engin
> =================================
> Computational Science & Engineering
> Koc University
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-----------------------------------------------------
XAvier Periole - PhD

NMR & Molecular Dynamics Group
University of Groningen
The Netherlands
http://md.chem.rug.nl/~periole
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