problem in Dynamics.py

[Konrad Hinsen]

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

There's a bug in MMTK, which makes it impossible to specify a
trajectory by file name in the integrator options. I haven't yet
decided whether I should fix it or disallow this feature in the
future; it is not trivial to implement correctly and not really
necessary.


A solution that works now and will work in the future is creating
the trajectory explicitly, i.e. change your code to

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

This also gives you more flexibility, you can for example create
a new trajectory (file mode 'w') or append to an existing one
(file mode 'a').

Konrad.
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