The first step for the polymer simulation is the 'Modeling.' The modeling is "Preparing information on which systems to perform simulations." In other words, modeling is 'Creating a small atomic system that can represent the real bulk system.' of course, it is ideal to replicate the actual experimental environment. But in an atomic-scale simulation environment, such attempts run into various limitations.
In many atomic-scale simulation codes such as LAMMPS, do the structural modeling under 'periodic boundary condition' in order to simulate an extensive system with a small computational amount. Therefore, the modeled structure in the 'Modeling module' is considered to be infinitely repeated with periodicity in the 'Simulation module' in the MatSQ environment. You can apply this to obtain meaningful results by modeling even only a few tens of molecules.
Based on this, it is necessary to disperse the polymer in the space of sufficient size when preparing a polymer simulation model.
Previous [MatSQ Tip] How to Model Polymer in 3D: Molecule Builder covered how to model polymers. The Molecule Builder module allows you to convert the polymer drawn as a 2D structural formula into 3D. In the Visualizer tab, you can see one converted polymer chain.
In order to imitate the actual system, it is necessary to create a 'simulation model' by adding several polymers in a cell with sufficient space. You can do this in the 'Structure builder' module.
This module tip will explain the 'Modeling for MD,' the first step in calculating polymer properties through molecular dynamics.
1. Polymer Modeling
First, model the desired polymer on the 'Molecule Builder' module. Please refer to the following link for the detail.
2. MD Model Preparation
Fill the polymers to the sufficient space on the Structure Builder module. It is recommended to create the cell with a length of several tens of angstroms or more so that adequate space can be made.
There are several ways to do this. But in this example, we are going to do this through the 'Edit' menu. Using the Edit menu, you can create a space of the desired size. Since the function does not support creating an empty cell, add any temporary atoms at a random position.
The next step is the essential step. Fill the desired number of polymers to the cell using the 'Fill' menu. Please note that checking on the 'Empty Structure' option to delete the existing atoms when filling the polymers.
You can also create a polymer blend system by adding multiple polymers during Fill if you have created numerous polymer chains through '+New Molecule' in Molecule Builder.
You can check the density on the 'Tool' tab of the mouse right-click setting window.
In this module tip, we learned how to create a polymer model for molecular dynamics simulations.
In the next module tip, we will find out how to make the thermally equilibrated state, which is the state that optimizes the model system with a certain temperature.
Thank you for your interest.
🍀Need more information?
[MatSQ Tip] Molecule Modeling in Materials Square
[MatSQ Tip] How to Model Complicated Molecule
[MatSQ Tip] How to Model Polymer in 3D: Molecule Builder
[MatSQ Tip] PolymRize: Predict polymer properties
LAMMPS : Molecular Dynamics Simulation for Polymer – Polymer MD