16 Dec
2007
16 Dec
'07
12:16 a.m.
>> while the second is the excluded volume restraint, a loop over all >> nonbonded pairs. Part of the nonbonded pair generation mechanism >> excludes bonded particles. Right, then the interesting question is how to do the non-bonded particle generation. From what I gather with modeller, the speedups compared to what I am describing come from using a proximity structure and caching the list rather than separating the bonded from the nonbonded computations. When generating the list you have to do a similar lookup to see if each pair is bonded? Or is there some more clever way of structuring things?