New Algorithms for Large Time-Step Molecular Dynamics Simulations and their Application to Protein and Nucleic Acids

9310295施利克，这项提议的目标是进一步扩展这项工作，以便它可以常规地应用于蛋白质和核酸。我们建议开发和实现一种新的算法，它结合了隐式积分和简正波技术。新算法将保持隐式格式继承的大时间步长稳定性，但也解决了运动的高频分量，从而可以保留高频模式的活动。通过在最先进的机器上并行实现，这将使以100飞秒量级的时间步长进行模拟成为可能；然后总模拟时间将接近毫秒范围。

9310295 Schlick The goal in this proposal is to extend this work further so that is can be applied routinely to protein and nucleic acids. We propose to develop and implement a new algorithm that combines implicit-integration and normal-mode techniques. The new algorithm will maintain the large time-step stability inherited in the implicit scheme, but also resolve the high-frequency components of the motion so that the activities of high-frequency modes can be retained. With parallel implementations on state-of-the-art machines, this will make possible simulations at time-steps of order 100 femtoseconds; the total simulation time will then approach the millisecond range.