A3. Working with Polymers
TEAMFF can be used to prepare simulations of molecular systems. In this section, we use polymer to see how it works.
If you just start DFF, use File/Recent Project to open the tutorials project. Navigate to the project root folder, right-click, and select Refresh. This will reload all files in this project.
We are using the TEAMFF database in this and following lessons. For exercises, we are using the database come with the tutorials. This is done by use the TEAMFF/Admin command to set up the database. In the dialog, use Browser to find the database provided with the Tutorials at Tutorials/database/TEAMFF.dffdb. The dialog shows force field tables of selected force field type. Select "TEAM" force field type and "TEAM-General" force field to use. Click "OK" to close this dialog.
Working on Polymer and LAMMPS
- In the subfolder tutorialA3_useTEAMFF, there is a polymer mode that has been prebuilt and converted to the MSD format. Double-click on this model to load the structure:
Note that this model has a low density (0.4587), which can be displayed by clicking “Property” in the toolbar. We will compress this model to a density closer to the experimental value.
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Click TEAMFF/Assign command. This dialog lists the database and force field selected (TEAM-General). The "Output" field lists the file name to be used for the output force field. Unselect Click OK to assign force field parameters. When the job is done, a force field table appears. Review and close the force field table.
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Select this model, open Edit/Charge Group to assign charge groups, and click Go to assign the charge groups automatically. Leave the "Cross bond charge" to be zero, click Compute command. When the job is completed, the dialog shows 505 charge groups (scroll the display area to view). The largest group contains 7 atoms, the smallest group contains 3 atoms, and all groups have a total charge of zero charge. Click OK to close ths dialog.
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We now compress the model to a higher density state. Select the model and open Simulation/Molecular Dynamics. Select “NPT”, set “Pressure” to be “1000.0” MPa (very high for a rapid compression), set the “Equilibration steps” to be “100” and “Evaluation steps” to be “200”. Make sure “Screen View” is “On” and click OK.
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DFF displays density changes during compression. Step 4 can be repeated as needed. Every time a new MD job starts, a subfolder is created for the job. When the system approaches the targeted density (1.5), stop the job. The instantaneous configuration should approximate but not match the target density. To make an exact density of 1.5, we would need to reset the cell edge parameters. The required edge size X1 can be calculated from current edge size X0, current density D0 and target density D1 using the following equation:
For this system, the target edge size should be 35.82 for a density of 1.5. Select the model, open Build/Adjust PBC, enter the cell edge size, and click OK.
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Repeat a NVT simulation in DFF to relax the simulation box and verify that the density is indeed correct.
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Let's submit the simulation to LAMMPS. Selecting the prepared MSD and PPF files from Project Navigator, and clicking Simulation/LAMMPS, which starts the External Simulation window.
The model and force field files are loaded. Note that the option of “Apply T-factor to LJ terms” is selected, a new force field in which the LJ parameters are scaled according to the applied temperature will be made and used for this job. Select “NVT”, set “Steps” to “1,000” in order to see the results quickly, and note that the “Trajectory file name” is “polymer.dta”. Click OK.
- When the job is finished, a subfolder named as “polymer_LAMMPS” will be created in the Project Navigator. This folder contains the input and output files of this LAMMPS job. Examine the input and output files. Select “polymer.dta” and “polymer.msd” files from the Project Navigator, then click Simulation/Trajectory Viewer to bring up the following dialog box:
Click OK to start a new window that replays the trajectory. The trajectory is played in a new window, you can use the same viewing options of DFF to translate, rotate, and zoom the models on the trajectory window.