energy_data.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 energy_data.nlogn_use, energy_data.contact_shell is less than 8Å, the necessary number of cells is less than energy_data.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.

Automatic builds 2017-07-19