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A large scale molecular dynamics simulation code using the fast multipole algorithm (FMD): performance and

James A Lupo1, Zhiqiang Wang, Alan M McKenney

  • 1Materials Directorate, Air Force Research Laboratory, Wright-Patterson, AFB, OH 45433-7702, USA.

Journal of Molecular Graphics & Modelling
|October 26, 2002
PubMed
Summary
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We introduce fast molecular dynamics (FMD), a scalable code for large simulations using the fast multipole method to efficiently handle electrostatic interactions. FMD enables more realistic molecular dynamics simulations for complex systems.

Area of Science:

  • Computational chemistry
  • Molecular dynamics simulations
  • Scientific computing

Background:

  • Efficient handling of long-range electrostatic interactions is crucial for accurate large-scale molecular dynamics (MD) simulations.
  • Existing methods can be computationally expensive for systems with many atoms.

Purpose of the Study:

  • To present the performance and application of the fast molecular dynamics (FMD) code.
  • To demonstrate FMD's capability in simulating large molecular systems, including liquid crystals.

Main Methods:

  • Implementation of the three-dimensional fast multipole method (FMM) for O(N) calculation of electrostatic forces.
  • Performance testing on high-performance computing platforms (IBM SP2, SGI Origin 2000, CRAY T3E) using MPI.
  • Stability and accuracy validation through comparisons with direct calculations, NAMD2, and cell-multipole methods.

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Main Results:

  • FMD demonstrates efficient and scalable performance for large molecular systems.
  • The code effectively handles long-range electrostatic interactions, enabling more realistic simulations.
  • Stability tests confirm the reliability of the FMD method.

Conclusions:

  • Fast molecular dynamics (FMD) provides an efficient, object-oriented, and scalable solution for large-scale molecular simulations.
  • The integration of the fast multipole method significantly enhances the simulation of electrostatic interactions.
  • FMD is a valuable tool for studying complex molecular systems like liquid crystals and proteins.