If CUTOFF=6 is used, then GNORM=20 is recommended. Once the geometry is optimized using GNORM=20, the CUTOFF should be removed, and GNORM reduced to, e.g., GNORM=10.
The effect of CUTOFF on times and accuracy of prediction of geometry can be investigated by examining the statistics for the optimization of the positions of hydrogen atoms in Crambin, a small 642 atom, 46 residue protein with formula C202H315N55O64S6, see Table I. For a larger system, hexokinase, 2E2O, a medium-sized protein of 5717 atoms and 299 residues, C1448H3073N375O810S11, results for a 1SCF calculation are shown in Table II. Hexokinase contains 375 molecules of water.
|Table I: Crambin||Table II: Hexokinase|
|Cutoff||Time (s)||Ratio||Distortion (Å)||Distortion (Å)||Energy (Kcal/mol)||
|Cutoff||Time (s)||Ratio||Energy (Kcal/mol)||
For the rare occasions when finer control is needed, use CUTOF1 and CUTOF2.
In MOZYME calculations, the cutoff distance for polarization functions is set by CUTOF1=n.nn. Beyond that distance, electrostatic interactions are considered only as point charges. At distances less than that given by CUTOF1, electrostatic interactions are represented by a point-charge and three polarization functions. Default: For systems of less than 30 atoms, CUTOF1 is 1000 Ångstroms; for systems of 30 or more atoms, CUTOF1 is 10 Ångstroms.
In MOZYME calculations, the cutoff distance for two-electron two center and one-electron two center integrals is set by CUTOF2=n.nn. Below that distance, the interaction between two atoms is represented by the exact NDDO approximation. Above that distance, one-electron integrals that depend on the overlap are ignored, and two-electron integrals are simplified. Instead of using all 100 two-electron integrals between two heavy atoms, only seven are used. These represent the terms <ss|ss>, <ss|sx>, <ss|sy>, <ss|sz>, <sx|ss>, <sy|ss>, and <sz|ss>. At still greater distances, beyond CUTOF1, only the <ss|ss> term is used. Default: for systems of less than 30 atoms, CUTOF2 is 1000 Ångstroms; for systems of 30 or more atoms, CUTOF2 is 9.9 Ångstroms.