Micelle

Step 1 · Select Platform Manipulations

Model Generation is required before downstream steps

Model Generation

Model Simulation and Analysis

Step 2 · Generation Method

Step 3 · Choose Forcefield & Surfactants

All-atom: select surfactants from database or upload custom structures (GAFF2 parameterization).

Name	{{ selectGenerationMethod==='preformedModel' ? 'Ratio' : 'Count' }}	Action
{{ lip.displayName }}

No surfactant selected.

Upload one or more surfactant structures (.pdb .mol2 .sdf .gro .xyz, ≤ 25 MB/file). They will be parameterized to GAFF2 (GROMACS).

File	Display Name	Ratio	Net Charge	Charge Model	Action
{{ sf.file.name }}

No files selected.

Coarse-grained: choose surfactants from database (MARTINI2, etc.).

Name	{{ selectGenerationMethod==='preformedModel' ? 'Ratio' : 'Count' }}	Action
{{ lip.displayName }}

No surfactant selected.

Step 4 · Drug Input

SMILES

Choose files (e.g., .pdb, .mol2; only .pdb for MARTINI2 FF)

Top files (.itp in MARTINI2 FF)

Electrical Charge

Please add hydrogen atoms and define the charge for your molecule before submission.

Charge Model

Drug Numbers

Tip: You can compute by molar ratio or encapsulation ratio. Sometimes a two-turn generation helps: first for surfactant counts, then for drug counts.

Step 5 · Micelle Shape & Conditions

Radius (nm)

Length (nm)

Box Size (nm)

Temperature (K)

Model generation ~1–2 minutes; simulation varies with system size.

Run multiple rounds of Model Generation to obtain an ideal micelle model before Simulation and Analysis. For support contact um.formulationmm@gmail.com.