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1、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 ），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
2、 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 the Amorphous Cell button on the Modules toolbar and select Construction from the dropdown
3、list.,build an amorphous cell,build an amorphous cell,4. To relax the cell -Discover Setup,4. To relax the cell-Discover Minimizer,Modules | Discover | Dynamics,There are different types of molecular dynamics simulations and these are classified by the ensemble names, NVE, NVT, NPT, and NPH. The let
4、ters refer to: N = constant number of moles V = constant volume E = constant energy T = constant temperature P = constant pressure H = constant enthalpy,Modules | Discover | Dynamics,Select NVT from the Ensemble dropdown list and change the Temperature to 300,5. To run and analyze molecular dynamics
5、,select NVE from the Ensemble dropdown list. Change the Number of steps to 5000. Change the Trajectory Save option to Full and the Frame output every to 250 Make cell.xtd the active document. Click the Play button on the Animation toolbar,Right-click and choose Label from the shortcut men to open th
6、e Label dialog. Select the ForcefieldType property and click the Apply button.,Select Edit | Atom Selection from the menu bar.,Change the Select by Property to Forcefield Type. In the matches text field, type o1o and click the Select button. On the Label dialog click the Remove All button and close
7、the dialog.,On the Label dialog click the Remove All button and close the dialog.,select oxygen from the Choose sets dropdown list,mean square displacement (MSD) of the oxygen atoms with time,The Discover Analysis tool uses the client-server architecture to calculate the mean square displacement. A
8、new folder, cell Disco Mean squared displacement, is created and the cell.xcd document within this folder contains a plot of the mean square displacement (MSD) of the oxygen atoms with time. The value of the MSD for a given time reported in the chart is the average over all time intervals of that le
9、ngth and over all atoms in the set.,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
10、 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 whethe
11、r 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 men
12、u. 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,
