Building Markov State Models for Periodically Driven Non-Equilibrium Systems
主 题: Building Markov State Models for Periodically Driven Non-Equilibrium Systems
报告人: Dr. Wang Han (CAEP Software Center for High Performance Numerical Simulation)
时 间: 2015-05-12 16:00 - 17:00
地 点: 理科一号楼1365室
Biomolecular systems under non-equilibrium conditions like external fields have attracted increased interest recently. In this talk, we firstly introduce a non-equilibrium molecular dynamics (NEMD) simulation method that samples the non-equilibrium system in a statistically reliable and thermodynamically consistent way. Then we demonstrate the way to build the Markov state model (MSM) for the non-equilibrium systems under a periodic external driving. The MSM reproduces the essential long timescale conformational dynamics of the original system, and at the same time it does not require the ergodicity of each single molecular trajectory. Therefore, it does not only describes, but also provides more insightful understanding of the non-equilibrium system than the standard analyses of the molecular trajectories. Our methods are tested and validated by an example non-equilibrium system: The alanine dipeptide under periodic electric field.