Algorithm for Computing Dynamics of Molecules

The Newton-Euler Inverse Mass Operator (NEIMO) algorithm and software that implements the algorithm have been developed to reduce the amount of time needed to perform computational simulations of the dynamics of macromolecules. The NEIMO algorithm and the associated software are intended, in particular, for simulations of molecular motions at a space-time mesoscale, defined here as a length scale ranging from nanometers to micrometers and a time scale ranging from microseconds to milliseconds. Older molecular-dynamics algorithms and computer programs are not suitable for mesoscale simulations because they were formulated for the time scales, of the order of a microsecond or less, characteristic of such high-frequency degrees of freedom as stretching of molecular bonds.