Re. Tuzun et al., RECENT ADVANCES IN POLYMER MOLECULAR-DYNAMICS SIMULATION AND DATA-ANALYSIS, Macromolecular theory and simulations, 6(5), 1997, pp. 855-880
Significant advances in molecular simulation methodology over the past
decade have greatly reduced the traditional size-timescale bottleneck
in molecular dynamics calculations. The development of the geometric
statement function method allows for systems up to several hundred tho
usand atoms to be simulated for up to several nanoseconds in reasonabl
e times on standard workstations. For constant energy simulations, the
use of symplectic integrators ensures accurate dynamics, even at long
simulation times, without velocity or other artificial rescaling sche
mes. Finally, new methods of frequency estimation allow for accurate v
ibrational mode frequency calculations even in the presence of chaotic
motion on time scales twenty times shorter than the standard fast Fou
rier transform, with an additional improvement in the sensitivity of t
he results when initial dynamics conditions are carefully chosen.