分子动力学模拟实例-扩散系数-7.PPTVIP

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 the Amorphous Cell button on the Modules toolbar and select Construction from the dropdown list. build an amorphous cell build an amorphous cell 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 letters refer to: N = constant number of molesV = constant volumeE = constant energyT = constant temperatureP = constant pressureH = 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 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 the 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 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 Ana