[MMTK] Speeding Up Subset Energy Evaluation

[Rocco Moretti]

Hello all,

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.

Thanks for any help,
-Rocco

P.S. MMTK version 2.5.11 (I think) on Python2.4