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    • Justin MacCallum's avatar
      Precompute GBNeck terms · 31a9036a
      Justin MacCallum authored
      The previous version of this code would compute
      the values of d0 and m0 for every iteration. This
      was unnecessary as these values are fixed at the
      start of the calculation by the radii of the particles
      involved. This resulted in unnecessary computation
      and memory access that dramatically slowed simulations
      using the GBn or GBn2 solvation models.
      
      The new version pre-computes the values based on the
      radii that are present in the system. Linear interpolation
      is used, which is consistent with Amber. The previous
      version of OpenMM used cubic, which gives slightly
      different results.
      31a9036a