problem in Dynamics.py

Kenneth Geisshirt kneth@strubix.dk
Mon, 15 Feb 1999 09:47:10 +0100


On Fri, 12 Feb 1999, Victor Manuel Rosas-García wrote:

quimic> Traceback (innermost last):
quimic>   File "<stdin>", line 81, in ?
quimic>   File "/usr/local/mmtk/Dynamics.py", line 48, in __call__
quimic>     _dynamics.integrateVV(self.universe, f, p,
quimic> NetCDFError: Unknown error

Well, I'm running on a SGI (Irix 6.3) and I have a similar problem. My
code is:

--- md.py ---

#!/usr/local/bin/python

from mmtk import *

world = InfiniteUniverse(AmberForceField())
world.protein = Protein('insulin')

world.protein.writeToFile('test1.pdb')

world.initializeVelocitiesToTemperature(300.0*Units.K)

integrator = VelocityVerletIntegrator(world, delta_t = 1.0*Units.fs,
				      log = (0, None, 100, stdout,
					     ("energy", )),
                                      trajectory = (0, None, 10, "insulin.nc",
                                                   ("time", "energy", 
						    "configuration")))




integrator(steps = 1)

world.protein.writeToFile('test2.pdb')
--- end of md.py ---

The error message is:

Traceback (innermost last):
  File "./md.py", line 22, in ?
    integrator(steps = 1)
  File "/usr/local/lib/python1.5/mmtk/Dynamics.py", line 48, in __call__
    _dynamics.integrateVV(self.universe, f, p,
SystemError: NULL result without error in call_object

When I remove the trajectory stuff the program runs perfectly. 

My conclusion is that there is something wrong with the trajectory (==
netCDF) part. Please, Konrad, help us.

Best regards,
  Kneth

-----------------------------------------------------------
Kenneth Geisshirt, M.Sc., Ph.D.     Computational Scientist 
Structural Bioinformatics               Tel:  +45 4516 2804
Advanced Technologies                   Fax:  +45 4516 2802
http://www.strubix.com                     kneth@strubix.dk

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