3、周期性边界条件研究.ppt

第一章 绪论 第一章 绪论 1.7 Model System and Interaction Potential Analysis of the Potential Energy 1.7.1 Effective pair potential for spherical molecules 1.7.1.1 Hard-sphere potential 1.7.1.2 Square-Well potential 1.7.1.3 Yukawa potential 1.7.1.4 Lennard-Jones potential Codes for calculating the total potential 1.7.1.5 Potentials for ions 1.7.2 potential for macromolecules Bonded potential Angle-bend potential Bond-stretch potential Torsion potential 1.8 Reduced Units Reduced unit----continue Reduced unit----continue 1.9 Simulation Box and Its Boundary Conditions 1.9.1 Simulation box 1.9.1 Simulation box---continue 1.9.2 Periodic boundary condition 1.9.3 Computer code for periodic boundaries An alternative code for periodic boundaries 1.9.4 Computer code for minimum image convention 1.9.5 Non-periodic boundary methods Example for non-periodic boundary conditions-----study the active site of an enzyme * In most of this course, the microscopic of a system may be specified in terms of the position and momenta of a constituent set of particles. In this case the rapid motion of the electrons have been averaged out. Hamiltonian Kinetic energy Potential energy External potential Pair potential about 90% Three body contribution In FCC crystal, up to 10% Effective pair potential For the purposes of investigating general properties of liquids and for comparison with theory, highly idealized pair potentials may be of value. In this section , I will introduce hard-sphere, square-well, Yukawa and Lennard-Jones potentials, etc. is the diameter of hard spheres SW potential is the simplest one including the attractive forces and can be applied to inert gases and some non-polar substances, etc. When , it can be used to model Ar reasonably well. Yukwa potential can also be used to model plasma, colloidal particles, and some electrical interactions. For argon: V=0.0 DO 100 I=1,N-1 RXI=RX(I) RYI=RY(I) RZI=RZ(I) DO 100 J=I+1,N