Recent advances in polymer molecular dynamics simulation and data analysis

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 thousand atoms to be simulated for up to several nanoseconds in reasonable 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 schemes. Finally, new methods of frequency estimation allow for accurate vibrational mode frequency calculations even in the presence of chaotic motion on time scales twenty times shorter than the standard fast Fourier transform, with an additional improvement in the sensitivity of the results when initial dynamics conditions are carefully chosen.