| Abstract: | Molecular dynamics is the integration of a set of coupled differential equations describing the motion of atoms over time. These equations exhibit the unfortunate property of stiffness, that is, terms of the equations (the forces on the atoms) are defined on several scales—ranging from tens of kcal/mol/Å to thousands of kcal/mol/Å. Additional nonconservative and stiff effects occur when a distance cutoff is used for the electrostatics and nonbonded potentials. Because the first derivative at the cutoff is essentially infinite, small variations in positions will cause large variations in energy and violate conservation of energy. The effects are demonstrated in a small system of 125 isolated water molecules. It is possible to greatly reduce and nearly eliminate the stiff integration effects with an improved integrator. The nonconservative effects of the distance cutoff cannot be removed by changing the integrator. © John Wiley & Sons, Inc. |
