[MMTK] Normal Modes problem

Vasisht R. Tadigotla vasisht at eden.rutgers.edu
Tue May 31 18:08:33 CEST 2005


I'm trying to calculate the normal modes for yeast RNA polymerase II (PDB
code: 1NIK) using the deformation force field. I'm using the
deformation_modes.py file in the examples directory. The protein has ~3300
c-alpha atoms.

After applying the cutoff, it tries to calculate 780 low frequency normal
modes but the calculation doesn't finish even after 15 hrs. I'm using
MMTK-2.5.7 on Fedora Core 2. The machine is a P4 2Ghz with 512MB RAM.

Am I correct in assuming that the largest stored matrix in this case would
be 780x3x3300 ? Should I try and reduce the number of normal modes
calculated by increasing the cutoff ?

When I run the program on a similar machine but with 256MB RAM, i get a
MemoryError: Can't allocate memory for array

Traceback (most recent call last):
  File "normalmodes.py", line 24, in ?
    modes = SubspaceNormalModes(universe, subspace)
line 13, in __init__
    VibrationalModes.__init__(self, universe, temperature, basis)
line 129, in __init__
  File "/usr/local/lib/python2.4/site-packages/MMTK/NormalModes/Core.py",
line 141, in _forceConstantMatrix
    energy, force_constants = self.universe.energyAndForceConstants()
  File "/usr/local/lib/python2.4/site-packages/MMTK/Universe.py", line
646, in energyAndForceConstants
    e, g, fc = eval(0, 1, small_change)
line 231, in __call__
    force_constants = \
"/usr/local/lib/python2.4/site-packages/MMTK/ParticleProperties.py", line
448, in __init__
    self.array = N.zeros((self.n,3, self.n,3), N.Float)
MemoryError: can't allocate memory for array

Here I think it's allocating 3300x3 X 3300x3 size array, though I'm doing
a reduced normal modes calculation. Is there an upper limit on the size of
the protein I can do approximate normal modes on?


More information about the mmtk mailing list