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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.

Information
Last Update:2024/12/10

Official site

http://www.modylas.org/

License

MODYLAS licence

Availability

The K supercomputer, FX10, and general PC cluster (Linux/Unix)
Core Developers
  • Yoshimichi Andoh  (Nagoya University)
  • Noriyuki Yoshii  (Nagoya University)
  • Kazushi Fujimoto  (Nagoya University)
  • Hidekazu Kojima  (Nagoya University)
  • Atsushi Yamada  (Nagoya University)
  • Susumu Okazaki  (Nagoya University)
  • Kensuke Iwahashi  (Institute for Molecular Science)
  • Fumiyasu Mizutani  (Institute for Molecular Science)
Target substance/model

Any molecular aggregates, especially molecules in nanotechnology and biotechnology disciplines, for example, solutions, micelles, lipid membranes, proteins, polymers, and viruses.
Physical quantities that can be computed

Orbitals, structures, and thermodynamic quantities such as free energy.
Methodology

Molecular dynamics method
Parallelization

Parallel computing by MPI and OpenMP is supported. The number of processes for MPI parallel computing is restricted to 2^n (n: positive integer) in the latest version released on the Web. The number of threads for OpenMP parallel computing is arbitrary.

Parallel computing by GPGPU is supported at the level of OpenACC in a development version, which has not been released yet.

Parallel computation using Xeon-Phi is being developed (supported as a JHPCN project).
Related keywords
Document

Y. Andoh, et al., J. Chem. Theo. Comp., 9, 3201-3209 (2013)
Other

This package includes various methods required for the molecular dynamics calculation of materials in nanotechnology and biotechnology. Highly efficient massively parallel computing is possible, and extended simulation is possible for systems comprising tens of thousands of atoms up to around 10 million atoms. The software can also calculate free energy.
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