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MODYLAS

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MODYLAS is a highly parallelized general-purpose molecular dynamics (MD) simulation program appropriate for very large physical, chemical, and biological systems. It is equipped most standard MD techniques including free energy calculations based on thermodynamic integration method. Long-range forces are evaluated rigorously by the fast multipole method (FMM) without using the fast Fourier transform (FFT) in order to realize excellent scalability. The program enables investigations of large-scale real systems such as viruses, liposomes, assemblies of proteins and micelles, and polymers. It works on ordinary linux machines, too.

Large-Scale Molecular Dynamics Simulation of All Atoms of an Adhesive Interface Using MODYLAS

Akira Shimazu (Nitto Denko Corporation)
Lamination of materials using adhesives is an indispensable technique in manufacturing. One of the keys to understanding the adhesion mechanism during lamination is gaining insight into the behavior of molecules at the adhesive interface. Large-scale molecular dynamics computation is a simulation technique that can address this task by simulating a realistic system. However, the computational demand of performing a large-scale all-atom molecular simulation for high-molecular weight adhesives would be far too excessive for computers available in a general laboratory. This research, therefore, used MODYLAS [1] along with the “K” supercomputer to develop techniques for large-scale molecular dynamics simulation for adhesive interfaces. MODYLAS is a molecular dynamics simulation software suited for large-scale and massively parallel computers, and adopts the fast multipole method (FMM) for the computation of long-range intermolecular electrostatic interactions. As shown in Fig. 1, MODYLAS maintains a high acceleration rate of 92.6% vs 64 nodes when 8,192 nodes are used to simulate the molecular dynamics of a 10 million atom life sciences model using K. In this research, we modified MODYLAS to enable computation of adhesive interface models, such as the one shown in Fig. 2, by using several thousands of nodes on K. This has enabled molecular simulations at adhesive interfaces involving several million atoms. It is hoped that applying this new technique to adhesive interfaces between various materials will lead to progress in our understanding of the adhesive mechanism.

[1] Y. Andoh, et al., Journal of Chemical Theory and Computation, 9 (7) 3201 (2013).

Figure 1: Benchmark testing result for MODYLAS running on K.

Figure 2: An example of adhesive interface model

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