[MMTK] Speeding Up Subset Energy Evaluation

Konrad Hinsen konrad.hinsen at cea.fr
Thu Mar 16 11:22:47 CET 2006

On Mar 13, 2006, at 17:53, Rocco Moretti wrote:

> In the program that I'm writing, I'm doing a number of subgroup- 
> subgroup
> interaction energy calculations using the Amber forcefield via
> universe.energy(subgroup1, subgroup2) calls. Unfortunately, these  
> calls
> seem to be painfully slow for the number of calls I'm looking to do.
>  From the profile results I'm getting, it seems that vast majority of
> the time is being spent in non-bonded interactions, specifically
> calculating the non-bonded pair list.
> Is there any way to speed up these calls? For my purposes, I only need
> to calculate the energy once per interacting pair (represented as
> MMTK.Collection or MMTK.Group objects), and the universe configuration
> stays the same between each energy call.

Do I understand correctly that you want to calculate the energies for  
many subgroups but with the same configuration? In that case, there  
isn't much to be done: what takes the time is the initialization of  
the force field evaluator, i.e. the compilation of energy terms that  
need to be taken into account. This is done once per subgroup pair,  
and in most applications this time is negligible compared to the many  
evaluation calls that are made for the same subgroup pair - but  
apparently not in your case.

Konrad Hinsen
Laboratoire Léon Brillouin, CEA Saclay,
91191 Gif-sur-Yvette Cedex, France
Tel.: +33-1 69 08 79 25
Fax: +33-1 69 08 82 61
E-Mail: konrad.hinsen at cea.fr

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