Case 3: Polymer Pure Substance (PET)

In this case, we explain how to construct a polymer chain system using Polyethylene Terephthalate (PET) as an example.

Target System

Polymer: PET (Polyethylene Terephthalate)
Composition: Degree of Polymerization (DP) 20 × 6 chains
Total Atoms: 2,172
Initial Target Density: 1.10 g/cm³

Calculation Code (run.py)

import fbtk

# 1. Initialize the Builder
builder = fbtk.Builder(density=1.10)

# 2. Add polymer (Specify repeating unit with SMILES)
builder.add_polymer(
    name="PET",
    smiles="*COC(=O)c1ccc(C(=O)*)cc1",
    count=6,
    degree=20
)

# 3. Build the system and perform relaxation
system = builder.build()
print("Starting relaxation for PET...")
system.relax()

# 4. Output results
system.to_file("pet_cell.mol2")
print("Done.")

Reviewing the Execution Log

Atoms:     2172       | Bonds:     2286
--------------------------------------------------------------------------------
       | Fmax           | FRMS           | Total E          |
Iter   | (kcal/mol/Å)   | (kcal/mol/Å)   | (kcal/mol)       | Status
--------------------------------------------------------------------------------
     0 |     53863.0553 |      6508.3338 | 1220889933258.8372 |
    10 |      6545.5622 |       379.3545 |      302101.6687 |
    20 |      1707.9974 |       169.7971 |      173901.9535 |
   ...
   980 |         6.7064 |         0.5306 |       16940.1926 |
   990 |         6.7195 |         0.5222 |       16919.0781 |
--------------------------------------------------------------------------------
=== Optimization Finished ===
Reason: Max-Iter
Total Time: 15.348s    (Avg: 15.348ms / step)
Final Energy: 16863.4483      kcal/mol
Final Fmax:   16.4322         kcal/mol/Å
Final FRMS:   0.5721          kcal/mol/Å
Min Distance: 1.0326          Å (Atoms 1931 and 1937)
--------------------------------------------------------------------------------

Result Explanation

Initial Polymer Structure Generation

FBTK internally constructs the topology for each segment and performs packing while considering appropriate conformations. Even for polymers containing rigid benzene rings in the main chain like PET, the system is output with initial collisions appropriately resolved. In this result, the Min Distance is 1.0326 Å, confirming that non-physical collisions have been sufficiently resolved within 1000 relaxation steps.