Porting molecular dynamics codes to AMD architectures

The need for Molecular Dynamics (MD) codes in this research is paramount. MD simulations provide critical insights into the behavior of molecules over time, allowing researchers to study dynamic processes, predict reaction mechanisms, and understand the physical properties of materials. Accurate MD simulations require significant computational power to handle the vast number of calculations involved in simulating molecular interactions and movements.

To meet these computational demands, the utilization of GPUs was crucial due to their parallel processing capabilities, which dramatically accelerate the performance of MD simulations compared to traditional CPU-based calculations. The project leveraged the experimental AMD MI100 GPU platform, introduced in 2020, accessed through SURF–ETP. AMD GPUs offer a competitive edge with their high processing power and efficiency, enabling researchers to perform more complex and detailed simulations within a reasonable timeframe.

 

AMD GPUs have become key accelerators in the field of high-performance computing. Since 2021, they have been introduced in large supercomputers, including the world's top-ranking Frontier and Europe's top-ranking LUMI systems. These supercomputers have set new benchmarks in computational capabilities, further highlighting the significance of AMD GPUs in advancing scientific research and complex simulations.

ETP contribution

  • SURF–ETP facilitated access to the experimental AMD MI100 GPU platform enabling computational calculations crucial for the research.
  • Continuous technical support to ensure seamless workflow.

Outcomes

This project, initiated in 2020, has made substantial advancements in computational chemistry and materials science, resulting in several published papers. The research covers a range of topics including ring currents in spin crossover complexes, TEG crystals, reaction mechanisms for oxidation, Diels–Alder reactions, gold aluminyl, and planar 4-carbon structures.

References

  • Patrick W. Fowler, Remco W.A. Havenith. "Periodoannulenes: A Generalized Annulene-within-an-Annulene Paradigm for Combined σ and π Ring Currents," The Journal of Physical Chemistry A, 2021, 125, 29, 6374–6383 (10.1021/acs.jpca.1c03170).
  • M. Holzheimer, J. S. Sinninghe Damsté, S. Schouten, R. W. A. Havenith, A. V. Cunha, A. J. Minnaard. "Total Synthesis of the Alleged Structure of Crenarchaeol Enables Structure Revision," Angewandte Chemie International Edition, 2021, 60, 17504 (https://doi.org/10.1002/anie.202105384).
  • Shahriar N. Khan, Alexa Griffith, Frank De Proft, Evangelos Miliordos, Remco W. A. Havenith, Dmytro Bykov, Ana V. Cunha. "[Fe4S4] cubane in sulfite reductases: new insights into bonding properties and reactivity," Physical Chemistry Chemical Physics, 2022, 24, 18543-18551 (10.1039/D2CP02124B).

  • Cunha, Ana V., Remco W. A. Havenith, Jari van Gog, Freija De Vleeschouwer, Frank De Proft, Wouter Herrebout. "The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling," Molecules, 28(2), 772 (10.3390/molecules28020772).

  • I. F. Leach, T. Speelman, C. Somsen, J. E. M. N. Klein, R. W. A. Havenith. "Revisiting sp2 Dilithio Methandiides: From Geometric Curiosity to Simple Bonding Description," Chemistry European Journal, 2023, 29, e202301911 (10.1002/chem.202301911).
  • A. V. Cunha, R. W. A. Havenith, C. Van Alsenoy, F. Blockhuys. "The Challenging World of Simple Inorganic Rings: Revisiting Roesky's Ketone and Roesky's Sulfoxide,"Chemistry European Journal, 2023, 29, e202302449 (10.1002/chem.202302449).
  • Ana V. Cunha, Francesca Milocco, Edwin Otten, Remco W. A. Havenith. "Changes in aromaticity of spin-crossover complexes: a signature for non-innocent ligands," Dalton Transactions, 2024,53, 2789-2796 (10.1039/d3dt03404f).
  • No labels