[Analysis Example] Simulation of Nafion membrane using Marini3 force field

MD calculation is a useful method for predicting material properties and is widely used for materials development. However, when dealing with slow-timescale phenomena such as polymer chain relaxation and phase separation, all-atom models are computationally expensive. Therefore, coarse-grained modeling can be used to perform calculations efficiently.
In this case, we used the Martini3 force field [1,2], which is a general-purpose coarse-grained force field, to calculate the polymer electrolyte (Nafion) membranes applied in fuel cells.

Nafion model is shown in Figure 1 (n=9, m=20, M=26924 g/mol). In the simulation cell, 20 molecules of Nafion and 5000 particles of water were placed This is equivalent to 92440 atoms when converted to an all-atom model, but the number of particles in the coarse-grained model is 10600, which reduces the computational cost. In addition, The Martini3 forcefield can be used to enhance the efficiency of the modeling process by retrieving the forcefield parameters from the database through appropriate segmentation.In the initial state, Nafion molecules were randomly arranged, and after relaxation by a short NVT calculation, an NPT calculation of 1 μs was performed at 350 K. Video 1 shows the animation during NPT calculation. You can see how the aqueous and Nafion phases separate to form a membrane structure which is suitable for ion-exchange.
This calculation was performed using GROMACS on Windows, and the calculation was completed in about 15 hours using 4 CPUs.

Figure 2 shows a diagram showing the position of the sulfo group. It can be seen that the sulfo groups (yellow particles) are abundant in the interface region with water. Figure 3 shows the calculation results of a larger model (160 Nafion molecules, 24,000 particles of water, 68,800 total particles). In a model of this scale, it is found that a complex water channel being formed.

Fig. 1: Modeling of Nafion by Martini3. The green circle corresponds to one coarse-grained particle.

Video 1: Visualization of the MD calculation results of the phase separation structure of Nafion and water in the first half of 600 ns with a large structural change. (Expanded by 2x)

Fig. 2: Isosurface of the volume fraction 0.5 of Nafion main chains, and molecular chains of he Nafion. Particles corresponding to sulfo groups are indicated by yellow spheres.

Fig. 3: (left) Martini3 model of Nafion membrane (68800 particle system). The length of cell is about 18nm. (right) Isosurface of the volume fraction 0.5 of water.