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

Tue Feb 12 19:56:04 CET 2008

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?

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?

Thanks in advance

Ozge Engin
Computational Science & Engineering
Koc University

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