Minary P, Tuckerman M E, Martyna G J
Department of Chemistry, New York University, New York, New York 10003, USA.
Phys Rev Lett. 2004 Oct 8;93(15):150201. doi: 10.1103/PhysRevLett.93.150201.
Although molecular dynamics methods are commonly used to drive biomolecular simulations, the technique provides insufficient sampling to impact studies of the 200-300 residue proteins of greatest interest. One severe limitation of molecular dynamics is that the integrators are restricted by resonance phenomena to small time steps (Delta t<8 fs) much slower then the time scales of important structural and solvent rearrangements. Here, a novel set of equations of motion and a reversible, resonance-free, integrator are designed which permit step sizes on the order of 100 fs to be used.
尽管分子动力学方法通常用于驱动生物分子模拟，但该技术提供的采样不足，无法影响对最感兴趣的200 - 300个残基蛋白质的研究。分子动力学的一个严重限制是，积分器受到共振现象的限制，只能采用小时间步长（Δt < 8 fs），比重要结构和溶剂重排的时间尺度慢得多。在此，设计了一组新的运动方程和一个可逆、无共振的积分器，允许使用约100 fs的步长。
