On 20/06/2012 12:03 AM, Isaure Chauvot de Beauchêne wrote:
Hi,
I'm trying to cluster 200 structure of a 20 aas peptide, by the
g_cluster "diagonalization" method. There is my command line:
*********************
g_cluster -f all_1-200.pdb -s ../pdb/FinalGSAFold_1.pdb -clid -cl
clusters.pdb -method diagonalization -o rmsd-clust.xpm -g cluster.log
*********************
I obtain these lines:
*********************
The RMSD ranges from -nan to -nan nm
Average RMSD is -nan
Number of structures for matrix 200
Energy of the matrix is -nan nm
*********************
If I run exactly the same job with changing for "gromos" method, I
obtain:
*********************
The RMSD ranges from 0.26113 to 1.22787 nm
Average RMSD is 0.622773
Number of structures for matrix 200
Energy of the matrix is 41.58 nm
...etc
*********************
Are there some case in which the diagonalization method is not usable?
What could be the reason of this fail?
I use VERSION 4.5.5.
Depending how GROMACS was configured, diagonalization may be using an
external library that might not be (dynamically) linked correctly,
leading to garbage results. Or your problem size is too large for your
available memory (and you are somehow not segfaulting). Diagonalizing a
200 x 200 matrix is not huge, but might not be possible on small
systems. I suggest trying a much smaller number of structures and
gradually increasing it to see what happens - or trying on a computer
with more memory. If everything fails, then the linking hypothesis might
be the best lead.
Mark
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