[MMTK] question on printing out all non-bonded interactions

Konrad Hinsen research at khinsen.fastmail.net
Thu Feb 2 08:33:56 UTC 2012

Naomi Fox writes:

 > I would like to efficiently print out each non-bonded atom pair interaction
 > and its associated LJ and coulombic potentials.
 > I have used the example the MMTK file 'Examples/Miscellaneous/
 > force_field_parameters.py' as a template.

That's a good start, and in fact the only way to obtain the parameters
at the Python level.

 > How do I get all the atom pairs with a distance below some cutoff?
 > Do the forcefields, for example Amber99, maintain some internal
 > list of these?

Not the force fields (they can't), but the energy evaluators do.  An
energy evaluator is the result of applying a force field to a
universe. Applying an energy evaluator to a configuration then yields
the energy.

The energy evaluators use a NonbondedList object to track pairs of
atoms within a given cutoff as they move in a Molecular Dynamics
simulation. NonbondedLists weren't meant to be used directly in user
scripts, which explains that their interface is not the most
convenient one, but it is certainly possible to do so and two examples
have been discussed earlier in this forum:



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: research AT khinsen DOT fastmail DOT net

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