[MMTK] Speeding Up Subset Energy Evaluation
roccomoretti at hotpop.com
Mon Mar 13 17:53:19 CET 2006
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,
P.S. MMTK version 2.5.11 (I think) on Python2.4
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