EnergyData.nlogn_use — select non-bond list generation algorithm

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 ${\cal O}(n^2)$ search or a cell-based algorithm which has $n \log n $ dependency of CPU time versus size $n$. The latter algorithm is used when the maximal difference in residue indices of the atoms in the current dynamic restraints is larger than EnergyData.nlogn_use, EnergyData.contact_shell is less than 8Å, the necessary number of cells is less than EnergyData.max_nlogn_grid_cells and fits in an integer without overflow, and there is sufficient system memory to store the cells. The default value is 15.