Before calculating dynamic non-bonded restraints, MODELLER determines which of the several routines is most appropriate and efficient for calculating the non-bonded atom pairs list. The user can use this variable to influence the selection, of either a straightforward search or a cell-based algorithm which has dependency of CPU timeversussize . The latter algorithm is used when the maximal difference in residue indices of the atoms in the current dynamic restraints is larger thanenergy_data.nlogn_useor when the box size for this algorithm would have to be larger than 8Å.

Ben Webb 2008-05-05