Case 2: Small Molecule Mixture (Water + Ethanol)

In this case, we construct a system mixed with two types of small molecules (water and ethanol) at a specific numerical ratio.

Target System

Composition:
- Water: 300 molecules
- Ethanol: 150 molecules
Total Atoms: 2,250
Initial Target Density: 0.80 g/cm³

Calculation Code (run.py)

import fbtk

# 1. Create each molecule object from SMILES
water = fbtk.Molecule.from_smiles("O", name="water")
ethanol = fbtk.Molecule.from_smiles("CCO", name="ethanol")

# 2. Initialize the Builder
builder = fbtk.Builder(density=0.80)

# 3. Add specified counts of each molecule
builder.add_molecule(water, count=300)
builder.add_molecule(ethanol, count=150)

# 4. Build the system and perform relaxation
system = builder.build()
print("Starting relaxation for Water + EtOH...")
system.relax()

# 5. Output results
water.to_file("water.mol")
ethanol.to_file("ethanol.mol")
system.to_file("water_etoh_cell.mol2")
print("Done.")

Reviewing the Execution Log

Atoms:     2250       | Bonds:     1800
--------------------------------------------------------------------------------
       | Fmax           | FRMS           | Total E          |
Iter   | (kcal/mol/Å)   | (kcal/mol/Å)   | (kcal/mol)       | Status
--------------------------------------------------------------------------------
     0 |     36477.1705 |      3459.2950 | 204596098964.3458 |
    10 |      1620.0353 |       134.2404 |       51220.1694 |
    20 |       813.1749 |        50.6762 |       24796.0682 |
   ...
   280 |         2.9743 |         0.2826 |        2533.5805 |
   290 |         1.5966 |         0.2099 |        2532.7015 | FRMS-Conv
--------------------------------------------------------------------------------
=== Optimization Finished ===
Reason: FRMS-Conv
Total Time: 5.678s     (Avg: 19.512ms / step)
Final Energy: 2532.7015       kcal/mol
Final Fmax:   1.5966          kcal/mol/Å
Final FRMS:   0.2088          kcal/mol/Å
Min Distance: 0.9979          Å (Atoms 1353 and 1359)
--------------------------------------------------------------------------------

Result Explanation

Initial Mixed State Structure

The Min Distance after relaxation is 0.9979 Å. It can be confirmed that a stable initial arrangement that does not “explode” before the formation of a hydrogen-bonded network has been obtained.