IMP Manual
for IMP version 2.14.0
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There a several pathways by which lists of spatially close pairs of particles are generated. In all cases, the lists are of close balls, that is pairs where the distance between the balls (defined by the coordinates and radius) is smaller than a threshold.
The three most common points of usage are
They all maintain an invariant which is that they have a list of close pairs that includes all that are within the requested threshold, but can contain others. They use this ability to have extra pairs in order to avoid rebuilding the list every time the model is perturbed. Specifically, they maintain a list that
threshold + 2*slack
of one another That way, until anything moves more than slack the list is still correct.They all use slightly different code paths but have an overall similar structure:
The update procedure uses one or more of: