[MMTK] MD with fixed atoms

Victor Muñoz chewaka.87 at gmail.com
Thu May 5 21:18:32 UTC 2011


Dear all,

Problem fixed. I just used the VelocityVerletIntegrator() instead of writing
it like in the MD integrator in python example. This way the universe keeps
updating and I can mantain fixed the atoms I want.

Now I have other problem when I try to save the MD. When I run the
Trajectory() script in the MMTK, I get the error 'NoneType' object has no
attribute 'name' in :

File
"/home/victor/bin/chimera_1.5.2/lib/python2.7/site-packages/MMTK/ChemicalObjects.py",
line 486, in _typeName
    return self.type.name

I'm trying to save the dynamics into the netCDF format using the universe
created by the UCSF chimera, as the dynamics already works. But neither
Conrad nor I knows which type do we need in order for Trajectory() to work.
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