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[MatSQ Tip] How to Model Polymer in 3D: Molecule Builder

2021-04-27 06:16:32

The PET bottle, which is common material around our living, has high transparency and good elasticity. These properties are not present in traditional materials such as ceramics, metals, and glass. These are also the characteristics of 'plastic', which is a base material of PET bottles. High moldability allows mass production system and good controllability of the materials' properties.

There are many kinds of plastics other than PET (polyethylene terephthalate), such as PP (polypropylene), PVC (polyvinyl chloride), and so on. They have a common feature that small unit molecules repeat many times to form a single molecule. Molecules with a molecular weight of 10,000 or more are called 'polymers'.

Nowadays, polymers are the essential components of numerous materials, ranging from household goods to automotive parts, medical supplies, electronic devices, and aerospace components. In general, polymer research involves selecting raw materials and synthesis methods, processing samples after synthesis, measuring physical properties, and optimizing processes.

However, discovering new polymers requires complicated synthesis procedures and a significant number of experiments. In each procedure, the researcher must continue to experiment based on their own experience or rely on the trial-and-error method. It takes a lot of time and effort to synthesize and experiment for all numbers of cases.

Computer simulation has emerged to overcome the limitations of traditional methods to find out polymer properties. In response to the increasing demands of computer-aided polymer research, MatSQ has added the 'Molecule Builder' module.

You can now draw molecules in 2D structural formula with the Molecule Builder module. This part is the same as the 'Draw Molecule' function of the Structure Builder module introduced in the previous module tip. You can also make 3D polymers by performing 3D optimization from 2D structural formulas.

This module tip will explain how to model polymers with the Molecule Builder.



Molecule Builder

You can add the 'Molecule Builder' module at the 'Modeling' tab of the 'Module selector (Import Module)', located at the bottom of the Work page.



The Molecule Builder module consists of the 'Ketcher' and 'Visualizer' tab. The 'Ketcher' tab allows you to draw structural formulas for molecular modeling. You can also add molecules by drawing structural formulas or writing SMILES in the same way as the Draw Molecule.

After the modeling of the monomer unit finishes, you should set the repeating part.

You can set that using the   button as a rectangular shape, but the lasso selection tool  enables a more complicated set the repeating unit.


After selecting the repeating unit by click-and-drag  using the lasso selection tool, click the  button to appear the above pop-up window.  Select the 'Multiple group' to the 'Type' option and enter the number you want in the 'Repeat count'. (note that it does not support over 999 atoms)


After completing the polymer modeling using the 2D structural formula, we should perform optimization by pressing the  button in the right list. This optimization process converts the 2D polymer into a 3D model. Molecule Builder also optimizes the structure by using forcefield[a] as the Draw Molecule menu of Structure builder. This step is essential to proceed with subsequent simulations.

You can create an additional new structure by pressing theNew Molecule button or duplicate the structure by clicking the button. If you want to erase the current structure and draw a new molecule, you can delete all atoms using the  menu or  button.


The following warning window will show up if the required optimization time exceeds 28 seconds or the molecular weight excluding hydrogen exceeds 1,500 g/mol.

The optimization job will be submitted to the cloud server when you click the 'Yes' button. In this time, the pre-charged credits will be deducted relative to the running time.


You can check the calculation progress status on the dashboard on the right of the top navigation bar.

When the calculation is complete, the job disappears from the list on the dashboard. Return to the Molecule Builder module and click the button to update the job status. When the calculation is completed normally, the Finished  icon is displayed.


Now you can check the 3D polymer in the 'Visualizer' tab.


Try to adjust the appearance at the 'Display' tab of the right-click setting window.


You can perform polymer simulations by connecting this Molecule Builder to simulation modules such as GAMESS and LAMMPS.



In this module tip, we learned how to model polymers using the new 'Molecule Builder' module. By connecting this structure to the simulation module, you can simulate the properties of the polymer. In addition, if you save the structure as a file in the Visualizer tab of the Molecule Builder module, you can import the file to the Structure Builder and calculate the properties of the polymer adsorbed on the metal surface.

MatSQ has been developing many functions to meet the demands of the chemical sector. Recently, the GAMESS module has been launched. The 'LAMMPS Polymer' template function, a theme-type MD module that can calculate polymer properties, is also scheduled to be released.

Simulate the properties of polymers using MatSQ's convenient GUI and fast computing environment!



Example Video



🍀Do you need more information?

[Modules] Molecule Builder

[MatSQ Tip] Molecule Modeling in Materials Square
[MatSQ Tip] How to model complicated molecule



[1] Halgren, T. A. (1996). Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. Journal of computational chemistry, 17(5‐6), 490-519.