Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
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...The PME method can be adopted to compute the electrostatic potential in real space and has been implemented in VMD (see Fig....
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...For this purpose, PME uses an interpolation scheme to distribute the charges, sitting anywhere in real space, to the nodes of a uniform grid as illustrated in Figure 3....
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...While this presents a serious impediment to other programs, NAMD’s message-driven architecture is able to automatically interleave the latency-sensitive FFT algorithm with the dominant and latencytolerant short-range nonbonded calculation.106 In conclusion, a simulation with PME will run slightly slower than a non-PME simulation using the same cutoff, but PME is the clear winner because it provides physically correct electrostatics (without artifacts due to truncation) and allows a smaller short-range cutoff to be used....
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...For a given accuracy, the computationally optimal choice of the parameter leads to a cost proportional to N3/ 2 in the standard computation, where N is the number of charges in the system.19 The particle–mesh Ewald (PME)20 method is a fast numerical method to compute the Ewald sum....
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...The most expensive parts of the PME calculation are the gridding of each atomic charge onto (typically) 4 4 4 points of a regular mesh and the corresponding extraction of atomic forces from the grid; both scale linearly with atom count....
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