MacroModel Reference Manual - ISP

Chapter 4: Operation CodesIf solvation is used in a minimization, the structure is minimized with analytical approximationsto surface areas, but the final energies reported use accurate numerical areas.If energies change substantially on reminimization or nonbonded updates, use the EXNBcommand to increase the nonbonded cutoff distances for electrostatics and van der Waals.Alternatively, update more frequently using arg7.arg1Minimization mode0.5 kJ/Å-mol.9 Truncated Newton (TNCG)—Superb method for flexible structures. There is nolimit on the number of atoms in the molecule when using TNCG. [24]. See arg6.10 Limited Broyden-Fletcher-Goldfarb-Shanno (LBFGS)—LBFGS can be specifiedby MINI arg1=10. Experiments so far have not shown superiority of this methodabove all others; however, we expect to improve the implementation as time goeson, as we feel this method has great potential.11 LTNCG—LTNCG is virtually identical to TNCG (MINI arg1=9), but it requires lessmemory and thus can be used on larger molecules. Differences between TNCG andLTNCG:TNCG is effectively single precision, but LTNCG is fully double precision.Because of the difference between the Hessian cutoff used by TNCG and LTNCG(see ARPK arg8), and the limited memory allowed for Hessian storage in LTNCG(see ARPK arg4), the sparse Hessian representation of TNCG and LTNCG mightdiffer. Nevertheless, LTNCG gives practically identical results with TNCG on smallto medium sized molecules (up to approx. 1000 atoms).For molecules for which both TNCG and LTNCG can be used, TNCG is faster by afactor of approx. 1.5 to 2.MacroModel 9.7 Reference Manual 53