6.14. MD ‣ Polymer Menu

The procedure for preparing the polymer system is as follows.

  1. Model the monomer and execute Register Monomer.
  2. Register the polymer using the monomer registered in 1 Homo Polymer builder, Block Polymer Builder, Random Polymer Builder.
  3. In the Polymer Cell Builder, construct the cell using the polymer registered in 2.

If you want to create a low molecular-polymer mixed system, create a polymer system by the above procedure and then add low molecules with Insert Molecules.

6.14.1. Register Monomer

register the monomer to use at Homo Polymer builder, Block Polymer Builder, Random Polymer Builder.The file is saved with the extension wmo in the save destination of the monomer file set by Settings. The wmo file is a mol2 file with Winmostar’s own comment added.

  1. Create the structure of the monomer (repeating unit) you want to register in the main window.
  2. Left click on Head and Tail 2 atoms, red circle’s marker, and call this function.
[Head], [Tail]
The number of the selected Head atom and Tail atom is displayed.
[Name]
Enter the name of the monomer to be registered.
[OK]
Register the monomer and close the window. A monomer file is created.
[Cancel]
Discard the settings and close the Register Monomer window.

6.14.2. Homo Polymer builder

Create a homo polymer for use with Polymer Cell Builder from the monomers registered with Register Monomer and register. It is stored in the save destination of the polymer file set with Settings with wpo extension. The wpo file is a mol2 file with Winmostar’s own comment added. The charge of the whole polymer is the product of the charge of the monomer (repeating unit) used and the degree of polymerization. Charges for atoms deleted by polymerization are equally allocated to the atoms of the whole polymer.

[Polymer Name]
Enter the name of the polymer to be registered.
[Polymerization Degree]
Specify the degree of polymerization.
[Monomer List]

Select the monomer to use.

[Display]
The selected monomers are displayed in the main window.
[Delete]
Delete the selected monomer file.
[Tacticity]
[Isotactic]
Make an isotactic polymer.
[Syndiotactic]
Make a syndiotactic polymer.
[Atactic]

Make atactic polymer.

[Racemo Ratio]
When selecting an atactic polymer, specify the racemism rate (0 <x <1.0).
[Head/Tail Configulation]
[Head to Tail]
Combine the head atom of the monomer and the tail atom by overlapping.
[Head to Head]
Combine the Head and Head atoms of the monomer. Also, combine the Tail and Tail atoms of the monomer.
[Build]
Register the polymer. A polymer file is created.
[Close]
Close the window.

6.14.3. Block Polymer Builder

Create a block polymer for use with Polymer Cell Builder from the monomers registered with Register Monomer and register it. It is stored in the save destination of the polymer file set with Settings with wpo extension. The wpo file is a mol2 file with Winmostar's own comment added. The way to assign electric charge is the same as Homo Polymer builder.

[Polymer Name]
Enter the name of the polymer to be registered.
[Polymerization Degree]
Specify the degree of polymerization.
[First Monomer]
Select the first monomer from the monomer list.
[Last Monomer]
Select the last monomer from the list of monomers.
[Internal Monomer]

Select an intermediate monomer from the monomer list. In [Number], enter the number of monomers.

[Number]
Specify the number of intermediate monomers.
[Add]
Reflect the set intermediate monomer name and number in the Internal Monomer List.
[Display]
Display the set intermediate monomer on the main window.
[Delete wmo File]
Delete the specified monomer file.
[Delete From List]
Remove the selected intermediate monomer from the list in the list.
[Build]
Register the polymer. A polymer file is created.
[Close]
Close the window.

6.14.4. Random Polymer Builder

Create a random polymer for use with Polymer Cell Builder from the monomers registered with Register Monomer and register it. It is stored in the save destination of the polymer file set with Settings with wpo extension. The wpo file is a mol2 file with Winmostar's own comment added. The way to assign electric charge is the same as Homo Polymer builder.

[Polymer Name]
Enter the name of the polymer to be registered.
[Polymerization Degree]
Specify the degree of polymerization.
[First Monomer]
Select the first monomer from the monomer list.
[Last Monomer]
Select the last monomer from the list of monomers.
[Internal Monomer]

Select an intermediate monomer from the monomer list. In [Number], enter the number of monomers.

[Ratio]
Specify the appearance rate (0 <x <1.0) of the selected intermediate monomer.
[Add]
Reflect the set intermediate monomer name and appearance rate in the Internal Monomer List.
[Display]
Display the set intermediate monomer on the main window.
[Delete wmo File]
Delete the specified monomer file.
[Sum of Ration]
The total value of the ratios listed in the Internal Monomer List is displayed.
[Delete From List]
Remove the selected intermediate monomer from the list in the Internal Monomer List.
[Definition of Ratio]
[Probability of Each Monomer]
Generate intermediate monomer according to appearance rate [Add]. The ratio of the final intermediate monomer does not necessarily correspond to the appearance rate.
[Proportion in Total Monomers]
The ratio of finally obtained intermediate monomer is proportional to the appearance rate [Add].
[Build]
Register the polymer. A polymer file is created.
[Close]
Close the window.

6.14.5. Polymer Cell Builder

Build a simulation cell using the polymer registered in Homo Polymer builder, Block Polymer Builder, and Random Polymer Builder. When using Solvate/Build Cell, it is difficult to create each molecule rigidly in the simulation cell, so it is difficult to create it with high density. However, when using this function, while executing energy minimization calculation using LAMMPS It can be created at a relatively high density for placement.

[Box Configulation]
[Density]
Specify the density.
[X-Axis Length]
Specify the rectangular parallelepiped cell's X direction length in Å. Or the length is displayed in Å.
[Y-Axis Length]
Specify the length of rectangular parallelepiped cell in Y direction in Å. Or the length is displayed in Å.
[Z-Axis Length]
The length of rectangular parallelepiped cell in Z direction is displayed in Å.
[Cubic Cell]
Specify a cube cell.
[Periodic Boundary Condition]
[X],[Y],[Z]
Toggle in the direction that imposes periodic boundary condition.
[Polymer Available]
[Number]
Specify the number of selected polymers.
[Display]
The selected polymer is displayed on the main window.
[Delete]
Delete the specified polymer file.
[Add]
The selected polymer is reflected in the Polymers Used list.
[Delete]
Remove the selected polymer from the Polymers Used list.
[MPI]

LAMMPS used for optimization at creation runs in MPI parallel.

[Processes]
Specify number of MPI ranks.
[non-bonded inter-atomic distance tolerance]
Specifies the minimum allowable distance between unbonded atoms. If it cannot be created with the specified tolerance, it will gradually reduce the tolerance, so it may not always be within the tolerance. Changes of the tolerance are output to the log.
[Build]
Create a simulation cell.
[Close]
Close the window.

6.14.6. Monomer allocation

We allocate registered monomers to DPD particles and acquire the molecular structure of all atoms MD.

6.14.7. Settings

Specify the folder to register the monomer and polymer.

[Monomer(*.wmo) Folder]
Specify the folder to save the monomer file.
[Polymer(*.wpo)Folder]
Specify the folder to save the polymer file.
[Dihedral Angle]

Specify the dihedral angle of polymerization.

[Random]
Set the dihedral angle at random.
[OK]
Save the settings and close the window.
[Cancel]
Discard the settings and close the window.