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Massively Parallel Implementation of Divide-and-Conquer Jacobi Iterations Using Particle-Mesh Ewald for Force Field

Dominique Nocito1, Gregory J O Beran1

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A new divide-and-conquer Jacobi iterations (DC-JI) solver accelerates polarizable force field calculations in large systems. This method enhances computational efficiency for molecular simulations, making complex chemical systems more tractable.

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Area of Science:

  • Computational chemistry
  • Molecular dynamics
  • Physical chemistry

Background:

  • Accurate molecular simulations require efficient calculation of self-consistent polarization.
  • Polarizable force fields are crucial for modeling condensed-phase systems.
  • Existing methods can be computationally intensive for large systems.

Purpose of the Study:

  • To develop and implement a faster solver for self-consistent polarization in large condensed-phase systems.
  • To adapt the divide-and-conquer Jacobi iterations (DC-JI) solver for periodic boundary conditions.
  • To improve the computational efficiency of polarizable force field simulations.

Main Methods:

  • Adaptation of the DC-JI solver for periodic boundary conditions with particle-mesh Ewald.
  • Implementation in the massively parallel Tinker-HP software package.
  • Acceleration of iterative convergence using direct inversion of the iterative subspace (DIIS).

Main Results:

  • The DC-JI/DIIS solver achieved approximately 20-30% faster computation of polarization equations compared to PCG and JI/DIIS algorithms.
  • Simulations on protein systems (10,000-175,000 atoms) showed significant speed-ups on hundreds of processor cores.
  • This resulted in 10-15% increased simulation time achievable per day.
  • DC-JI/DIIS provided more energetically robust solutions for a given convergence threshold.

Conclusions:

  • The DC-JI/DIIS solver offers a significant speed-up for polarizable force field calculations in large systems.
  • This advancement makes computationally robust polarizable force field simulations more feasible for complex chemical systems.
  • The enhanced efficiency facilitates larger-scale molecular dynamics simulations and analyses.