An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions.
Presented here is a method, the hierarchical charge partitioning (HCP) approximation, for speeding up computation of pairwise electrostatic interactions in biomolecular systems. The approximation is based on multiple levels of natural partitioning of biomolecular structures into a hierarchical set of its constituent structural components. The charge distribution in each component is systematically approximated by a small number of point charges, which, for the highest level component, are much fewer than the number of atoms in the component. For short distances from the point of interest, the HCP uses the full set of atomic charges available. For long-distance interactions, the approximate charge distributions with smaller sets of charges are used instead. For a structure consisting of N charges, the computational cost of computing the pairwise interactions via the HCP scales as O(N log N), under assumptions about the structural organization of biomolecular structures generally consistent with reality. A proof-of-concept implementation of the HCP shows that for large structures it can lead to speed-up factors of up to several orders of magnitude relative to the exact pairwise O(N(2)) all-atom computation used as a reference. For structures with more than 2000-3000 atoms the relative accuracy of the HCP (relative root-mean-square force error per atom), approaches the accuracy of the particle mesh Ewald (PME) method with parameter settings typical for biomolecular simulations. When averaged over a set of 600 representative biomolecular structures, the relative accuracies of the two methods are roughly equal. The HCP is also significantly more accurate than the spherical cutoff method. The HCP has been implemented in the freely available nucleic acids builder (NAB) molecular dynamics (MD) package in Amber tools. A 10 ns simulation of a small protein indicates that the HCP based MD simulation is stable, and that it can be faster than the spherical cutoff method. A critical benefit of the HCP approximation is that it is algorithmically very simple, and unlike the PME, the HCP is straightforward to use with implicit solvent models.
Anandakrishnan
Ramu
R
Department of Computer Science, Virginia Tech 2050 Torgersen Hall (0106), Blacksburg, Virginia 24061, USA.
Onufriev
Alexey V
AV
D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D009696:Nucleic Acids / Q000737:chemistry*; D011506:Proteins / Q000737:chemistry*; D011789:Quantum Theory
D009696:Nucleic Acids; D011506:Proteins