[MMTK] Segmentation fault, normal modes calculation

Konrad Hinsen hinsen at cnrs-orleans.fr
Thu Jan 11 12:00:30 CET 2007

On Jan 5, 2007, at 11:23, Lars Skjærven wrote:

> I am trying to calculate the normal modes of a large chaperon (GroEL/
> GroES complex, pdb code: 2cgt/1aon/1xck/2eu1). We know that these pdb-
> files have some missing residues, which we think may cause the
> problem. I have tried different methods, but they all return the same
> error. Namely "Segmentation fault". No other details are written to
> the screen. Running throught the gdb we found that it crashes at line
> 668 in MMTK_forcefield.c. This happens both om x86 and AMD 64 system.

The cause of the crash is a bug in MMTK, which is fixed in the public  
Mercurial archives. It concerns the handling of force constant  
matrices whose size exceeds 4 GB. Your system has 7854 atoms, the  
force constant matrix thus has 9*7854**3 elements or 8*9*7854**3 bytes.

Note however that the fix in MMTK by itself is not sufficient. Arrays  
 > 4 GB require Python 2.5 and NumPy. I have verified that with the  
latest MMTK + Python 2.5 + NumPy, the force constant matrix for your  
system is calculated. However, I cannot test if the computation of  
the normal modes succeeds, because I don't have any machine with  
sufficient memory to run the job without excessive thrashing.

My suggestion for handling your big protein is to switch to a  
different algorithm, which requires only two changes:

1) Change
	from MMTK.NormalModes import NormalModes, SubspaceNormalModes
	from MMTK.NormalModes import NormalModes,  

2) Change

      modes = SubspaceNormalModes(universe, subspace)


      modes = FiniteDifferenceSubspaceNormalModes(universe, subspace)

With that change, the huge force constant matrix is never calculated.  
Instead, numerical differentiation is used to calculated only the  
1734**2 force constant matrix for the selected Fourier subspace. This  
is somewhat less accurate, but uses only 22 MB for the force constant  

Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: hinsen at cnrs-orleans.fr

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