6.11. MD ‣ Polymer Menu

The procedure for preparing the polymer system is as follows.

Model the repeat unit and execute Register repeat unit.

Register the polymer using the monomer registered in 1 Homo Polymer builder, Block Polymer Builder, Random Polymer Builder.

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.

6.11.1. Register repeat unit

register the repeat unit 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.

Create the structure of the repeat unit you want to register in the main window.

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.

[OK]
Enter a registration name for the repeating unit, register the repeating unit and close the window. A monomer file will be created.

[Cancel]
Discard the settings and close the Register Monomer window.

6.11.2. Homo Polymer builder

Create a homo polymer for use with Polymer Cell Builder from the repeat units registered with Register repeat unit 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 (repeat unit) used and the degree of polymerization. Charges for atoms deleted by polymerization are equally allocated to the atoms of the whole polymer.

[Degree of Polymerization]
Specify the degree of polymerization.

[Repeat Unit]
Display selected repeat units.

[Display]
Display selected repeat units.

[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 repeat unit and the tail atom by overlapping.

[Head to Head]
Combine the Head and Head atoms of the repeat unit. Also, combine the Tail and Tail atoms of the monomer.

[Build]
Register the polymer. A polymer file is created.

[Close]
Close the window.

6.11.3. Block Polymer Builder

Create a block polymer for use with Polymer Cell Builder from the monomers registered with Register repeat unit 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.

[First Repeat Unit]
Select the first repeat unit from list.

[Last Repeat Unit]
Select the last repeat unit from the list.

[Middle Repeat Unit]
Select an intermediate repeat units from the repeat unit list. In [Number], enter the number of repeating.

[>>Add>>]
Registers the selected repeat unit in the list.

[<<Delete<<]
Delete selected items from list.

[Display]
Display selected repeat units.

[Delete]
Delete selected repeating units.

[Build]
Creates a polymer based on the contents of the list. A polymer file will be created.

[Close]
Close the window.

6.11.4. Random Polymer Builder

Create a random polymer for use with Polymer Cell Builder from the monomers registered with Register repeat unit 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.

[Degree of Polymerization]
Specify the degree of polymerization. Enter the number including the beginning and the end.

[First Repeat Unit]
Select the first repeat unit from the list. If you want to assign the first repetition unit randomly, leave blank.

[Last Repeat Unit]
Select a tail repeat unit from the list. If you want to assign the tail repeat unit randomly, leave it blank.

[Middle Repeat Unit]
Select an intermediate repeat unit from the list.

[>>Add>>]
The set repeat unit name and occurrence rate (0 < x < 1.0) will be reflected in Middle Repeat Unit.

[<<Delete<<]
Delete selected items from list.

[Display]
Display selected repeat units.

[Delete]
Register the set repeting unit name and occurrence rate (0 < x < 1.0) in the list.

[Sum of Ration]
The total value of the ratios listed in the Internal repeat unit List is displayed.

[Definition of Ratio]

[Probability of Each Monomer]
Generate intermediate repeat unit according to appearance rate [Add]. The ratio of the final intermediate repeat unit does not necessarily correspond to the appearance rate.

[Proportion in Total Monomers]
The ratio of finally obtained intermediate repeat unit is proportional to the appearance rate [Add].

[Number of Patterns]
Specifies the number of patterns of polymers.

[Use Specific Random Seed]
If you want to use a specific random number type, check the box and specify the value. If not specified, you will get a pattern with a different structure.

[Build]
Create polymers based on the contents of the listings. Polymer files will be created under the polymer name folder for the number of patterns.

[Close]
Close the window.

6.11.5. 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 polymers 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. The internal process is as follows

Place each polymer in a straight line.

Only the main chain of each polymer is extracted for structural optimization.

Structure optimization is performed by adding side chain atoms that can be added to the extent that each atom is not in contact with each other.

Repeat 3 until all atoms have been added.

[Polymer Available]

[Display]
Show the selected polymer.

[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.

[Simulation Cell] tab

[Set Density]
Specify the density.

[Set Dimensions]
Specify a cube cell.

[Cubic Cell]
Specifies the length of a rectangular cell in each direction.

[Periodic Boundary Condition]

[X],[Y],[Z]
Toggle in the direction that imposes periodic boundary condition.

[Options] tab

[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.

[Randomly select random polymers to be used]
For Random Polymer, randomly select the polymer to be used. If it is not checked, use them in order.

[Use Specific Random Seed]
If you want to use a specific random number seed, check the box and specify the value. If not specified, you will get a different structure each time.

[Do not twist each polymers]
Place each polymer in a straight line.

[Build]
Create a simulation cell.

[Close]
Close the window.

6.11.6. Map Repeat Unit

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

6.11.7. 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.

[OK]
Save the settings and close the window.

[Cancel]
Discard the settings and close the window.