[MMTK] bug in Trajectory?

Konrad Hinsen hinsen at cnrs-orleans.fr
Sat Jan 12 14:32:59 UTC 2008

On 09.01.2008, at 00:09, Paul de Mascureau wrote:

> So my conclusion is that MMTK is creating a bad description, or at  
> least a
> description that cannot be used by xMoldyn. Has anyone already had  
> this
> problem?

This is due to a minor bug in the HarmonicOscillatorForceField  
example, which is fixed now in the Mercurial repository (and will be  
in the next release, of course):


However, fixing this bug was only the first step to make everything  
work. There was a long-standing problem with using non-standard force  
fields (force fields that are not part of MMTK itself) with  
trajectory files. The system description in the trajectory would  
systematically raise an exception because MMTK didn't know from where  
to get the force field.

In the current version (again the Mercurial repository), this is  
fixed. The full path to the force field class is recorded in the  
trajectory, and the code that reconstructs the system when the  
trajectory is read imports the module(s) in order to create the force  
field object. The only requirement is that the module containing the  
force field class must be importable, i.e. be located on sys.path.  
This also works from xMoldyn, provided of course that the system you  
run xMoldyn on has this very latest MMTK version installed.

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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