Model building, equilibration and validation of a 105 lipid Nonoxynol 10 micelle

Nonyl phenol ethoxylated decyl ether (also Nonoxynol 10, or Tergitol NP-10) is a nonionic, water soluble surfactant. An aggregation number of 105 lipids and an ellipsoidal shape has been reported (Zhang R., Somasundaran P., Langmuir. 2004 Sep 28;20(20):8552-8, doi:10.1021/la049295a [Reference]).

Molecule:


The initial model building and subsequent equilibration were performed with Micelle Maker.

Because of the enormous size of the system (291229 atoms, box size 147^3 Å) and the resulting high computational costs, Nonoxynol 10 is not available in the Micelle Maker web service. However, we provide the parameter files for AMBER and the Micelle Maker results instead.

Parameters:
The nonionic head group of Nonoxynol 10 was described by the GAFF2 force field as implemented in AMBER16, the hydrophobic tail was described by the GLYCAM library similar to all other lipids available in the Micelle Maker web service. Partial charges were calculated in the gas-phase at the HF/6-31G* level of theory, using Gaussian09 rev. D.01 and the standard RESP fitting procedure.

LEaP parameter files for Nonoxynol 10:
Download library file
Download frcmod file

Micelle after equilibration:


Results from initial model building and equilibration:
Download here

Molecular dynamics simulation (MD):
The validation simulation and subsequent analysis was done in the same way as described for all other lipids described in the Micelle Maker reference.

Micelle after 100ns MD simulation:


Radius of Gyration:


Eccentricity:

Krüger, D. M., Kamerlin, S. C. L., Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations, ACS Omega, 2017, 2 (8), pp 4524–4530, DOI: 10.1021/acsomega.7b00820. [Reference]