Pregledni rad
https://doi.org/10.31784/zvr.13.1.17
Extending fast multipole method in exascale molecular dynamics for non-cubic simulation boxes
Matea Turalija Reščić
orcid.org/0000-0002-0109-1245
; Sveučilište u Rijeci, Medicinski fakultet u Rijeci, Rijeka, Hrvatska
*
* Dopisni autor.
Sažetak
Over the past decade, computer simulations have become an indispensable tool for studying and predicting physical and chemical processes. In particular, molecular dynamics simulations play an important role in the study of biological systems such as proteins, membranes, and nucleic acids. The increasing complexity of these simulations requires a large amount of computing resources and the development of new, more advanced methods. Today, we can study complex systems involving millions of atoms and solve problems in many scientific fields. In addition, there is hope for a better understanding and discovery of new drugs for many diseases such as viral infections or autoimmunity. In this paper, the application of the fast multipole method to molecular dynamics simulations in non-cubic simulation boxes is analyzed. The results show that this method is effective for cubic and slightly non-cubic boxes with a small number of particles, while larger deviations in the calculated energies from the reference ones occur for a larger number of particles and for more pronounced non-cubic boxes. In order to reduce the error in energy calculation, a correction factor was introduced depending on the volume of the box and the number of particles, which achieved a noticeable improvement in the precision of the method in terms of calculated energy.
Ključne riječi
molecular dynamics simulation; particle mesh Ewald; fast multipole method; GROMACS
Hrčak ID:
331497
URI
Datum izdavanja:
18.6.2025.
Posjeta: 900 *