分子动力学模拟实例扩散系数.ppt

MSD Expand the Dynamic node and select Mean squared displacement You must specify which document you want to perform the analysis on. A logical trajectory document consists of one or more trajectories so you will use this to specify your trajectory document On the Discover Analysis dialog, select oxygen from the Choose sets dropdown list. Click the Analyze button and close the dialog. 6. To export data and calculate the diffusivity The final part of this tutorial involves the use of an external spreadsheet or charting package. You will use it to check whether the calculation of the mean square displacement has been successful and then to calculate the diffusivity coefficient from the mean square displacement. You should copy and paste the chart document into your chosen spreadsheet package. Right-click in the plot, and select Copy from the shortcut menu. Open a new spreadsheet, right-click in the spreadsheet and select Paste from the shortcut menu. At this point in a real calculation, you would check to see if your calculation has produced reliable results. You can do this by plotting log(MSD) against log(time) and, if your calculation has converged, you should obtain a straight line. If you do not have a straight line, you should run the production stage of the calculation again. Plot MSD vs. time. Calculate the line of best fit of the graph using linear regression, y = ax + b. Note down the slope, a. D = a/6 THANK YOU SUCCESS * * 可编辑 可编辑 可编辑 分子动力学模拟实例 聚合物中分子扩散系数的计算模拟 分子动力学做扩散系数有两种方法：1. 计算体系的均方位移（Mean square displacement ＭＳＤ），然后根据Einstein关系求得扩散系数；2. 计算体系的速度自关联函数（Velocity auto-correlation function VACF)然后再通过Green-kubo关系计算体系的扩散系数  1、Getting started Begin by starting Materials Studio and creating a new project. Open the New Project dialog and enter polymer_gas as the project name, click the OK button. The new project is created with polymer_gas listed in the Project Explorer. 2. To set up the initial structures 3. To build an amorphous cell Click th