清华“分子动力学模拟入门.ppt

CASE(1) - Couette Flow z CASE(2) - Contact Angle Simulation Mass: m[1]=1, m[2]=8, m[3]=0.8 L=25.05, W=6.56 H=10.29 T=1.2 i, j=1,2,3, 1 – red fluid, 2 -- wall, 3 – green fluid V CASE(3)- Rayleigh-Taylor instability generation(重力场) Dzwinel, W., Alda, W., Pogoda, M., and Yuen, D.A., 2000, Turbulent mixing in the microscale: a 2D molecular dynamics simulation, Physica D, Vol. 137, pp. 157-171. Fig. 1. The snapshots of MD simulations of the R–T instability for two particle systems: (A) closed; (B) open (the heavy fluid is coloured in light grey while the lighter one is dark grey, the black part of the figure is empty, i.e., it does not contain particles). Fig. 2. The effect of converging geometry obtained by MD simulation of one million particles in the microscale. 0.5 μm CASE (4)Typical translocation event A 1.4V bias applied to membrane. 20 base-pair fragment of double stranded DNA placed in front of a nanopore. End of DNA nearest to the pore is pulled into the pore by its charged backbone (a,b) System reaches a meta-stable state (c) and translocation halts. Base-pairs start to split. Some freed nucleotides adhere to pore surface. Voltage increased momentarily to drive system out of metastable state. DNA exits pore. One of the bases holds firmly to the pore surface. After 50ns, most of DNA has left pore. Nine of twenty base pairs are split. Bubble nucleation on solid surfaces Maruyama, S, and Kimura, T., 2000, A Molecular Dynamics Simulation of a Bubble Nucleation on Solid Surface, Heat and Technology, Vol. 18, pp. 69-73. Molecular transport in droplets Maruyama, S., Matsumoto, S., and Ogita, A., 1994, Surface Phenomena of Molecular Clusters by Molecular Dynamics Method, Thermal Science and Engineering, Vol. 2, No. 1. Full View Sliced View Void View 参考书目 D. C. Rapaport. The Art of Molecular Dyna-mics Simulation. LAMMPS 开源的MD模拟软件 版本 Fortran77＋MPI Fortran90＋MPI C++＋MPI 可单机运行，也可并行计算 可以模拟气体、液体、固体 Samples MD Program crystal.f90 生成粒子 生成数据文件 md1.f90 MD模拟 * * 气体与