分子动力学模拟方法技巧.ppt

分子动力学方法基础： 分子动力学方法特征： 分子动力学是在原子、分子水平上求解多体问题的重要的计算机模拟方法，可以预测纳米尺度上的材料动力学特性。 通过求解所有粒子的运动方程，分子动力学方法可以用于模拟与原子运动路径相关的基本过程。 在分子动力学中，粒子的运动行为是通过经典的Newton运动方程所描述。 分子动力学方法是确定性方法，一旦初始构型和速度确定了，分子随时间所产生的运动轨迹也就确定了。 分子动力学的算法：有限差分方法 优点： 1、精确，误差O(Δ4) 2、每次积分只计算一次力 3、时间可逆 缺点： 1、速度有较大误差O(Δ2) 2、轨迹与速度无关，无法与热浴耦联 优点： 1、提高精确度 2、轨迹与速度有关，可与热浴耦联 缺点： 1、速度近似 2、比Verlet算子多花时间 Verlet三种形式算法的比较： 微正则系综分子动力学(NVE MD) 正则系综分子动力学(NVT MD) Potential Energy = Stretching Energy + Bending Energy + Torsion Energy + Non-Bonded Interaction Energy 这些方程与描述原子或键各种不同行为的参数就构 成了力场， force-field. Bond Stretching Energy Bending Energy The “Hookeian” potential Torsion Energy Non-bonded Energy Basic form requires an O(N2) calculation efficiency can be introduced to reduce to O(N3/2) good value of a is 5L, but should check for given application can be extended to sum point dipoles Other methods are in common use reaction field particle-particle/particle mesh (better for larger systems) fast multipole (better for larger systems) 1. 复杂分子体系的势能函数形式： UFF, OPLS, Amber, CVFF, Compass 分子模拟方法补充介绍： kb is the spring constant of the bond. r0 is the bond length at equilibrium. Unique kb and r0 assigned for each bond pair, i.e. C-C, O-H k? is the spring constant of the bend. ?0 is the bond length at equilibrium. Unique parameters for angle bending are assigned to each bonded triplet of atoms based on their types (e.g. C-C-C, C-O-C, C-C-H, etc.) kb and k? broaden or steepen the slope of the parabola. The larger the value of k, the more energy is required to deform an angle (or bond) from its equilibrium value. A controls the amplitude of the curve n controls its periodicity shifts the entire curve along the rotation angle axis (?). The parameters are determined from curve fitting. Unique parameters for torsional rotation are assigned to each bonded quartet of atoms based on their types (e.g. C-C-C-C, C-O-C-N, H-C-C-H, etc.) A determines the deg