MD讲义.pptVIP

Course Objectives Introduce the basic algorithm of molecular dynamics simulation and useful tricks. Understand the algorithm of long-range interaction. Learn how to model macromolecular system by implementing MD simulation. Write your own parallel codes using MPI for Beowulf cluster. Gain familiarity with typical MD simulation packages: DLPLOY. Course Outline and time schedule MD – the Fundamental: 11.05 Tricks in MD of polymer: 11.12, 11.19 DLPOLY packages –Part I: 11.26 Ewald Algorithm: 12.03 DLPOLY packages –Part II: 12.10 SPME Algorithm: 12.17 MD – the Fundamentals Finite difference of Newton motion equations Periodic boundary conditions Force field: atomic and molecular system Sampling from ensembles Code analysis: Bead-spring chain Finite difference of Newton motion equations Periodic boundary conditions Force field: atomic and molecular system NVT分子动力学算法 Sampling from ensembles Code analysis: Bead-spring chain Project 1: Persistence Length of Freely Rotating Chain Project 2: Form factor of ideal chain * * Tuesday, 1:00 PM, Room 718, 705 0 E LJ R R0 2-1/6R0 -D0 截断 R 0 0 U FENE r r 大分子体系模拟 分子动力学算法 NVT NPT NEMD NVE 分子力学、经验力场 DREIDING MM2/MMP2 CHARMM AMBER 1 规定初始位置、初始速度 2 计算第n+1步的位置 3 计算第n+1步的速度 4 计算标度因子 5 对所有速度进行标度 速度标度恒温算法 1 规定初始位置、初始速度 2 计算第n+1步的位置 4 计算第n+1步的速度 3 计算摩擦系数 Nose-Hoover恒温算法 键伸缩Bond Stretching 键角弯曲Bond Bending 键扭转 Torsion 键翻转Inversion Kinetic energy, potential energy Temperature, pressure Chemical potential Quantities from fluctuations Pair distribution function Diffusion coefficient Shear viscosity * * * * *