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• W2336528065 abstract "Introduction Molecular Dynamics (MD) is of central importance to computational chemistry and its myriad applications. Here we show that MD can be implemented efficiently on a COTS FPGA bard, and that speed-ups from 31× to 88× over a PC implementation can be obtained. The amount of speed-up depends on the stability required, with the upper end of that range being viable in many cases. MD is an iterative technique that runs in phases: the forces on each atom/molecule are computed, then applied using equations of motion, for example, Verlet. Shown is the WildstarII-Pro board from Annapolis Micro Systems, Inc, with two Xilinx Virtex-II-Pro XC2VP70 -5 FPGAs. Methods We implement the non-bonded forces, Lennard-Jones and Coulombic, with cut-off in a periodic model. Results Extensions Implementation Fixed point is used. Precision varies as per configuration. Data are scaled to maintain near maximum resolution throughout the computation while bounding the data-path size. The force calculations use table look-up with interpolation. Since the Force and Verlet Pipeline arrays work iteratively, they share some hard multipliers Our work differs from previous approaches in that we combine the following: on the hardware side, that we use a COTS board; on the implementation side, that we model the Coulombic as well as the LJ term, and that we support the simultaneous modeling of multiple types of molecules. We have also investigated precision/accuracy tradeoffs. ji ji ab ji ab i j ab ab LJ i r r r F r r r ⎪⎭ ⎪ ⎬ ⎫ ⎪⎩ ⎪ ⎨ ⎧ ⎟ ⎟ ⎠ ⎞ ⎜ ⎜ ⎝ ⎛ − ⎟ ⎟ ⎠ ⎞ ⎜ ⎜ ⎝ ⎛ =∑ ≠ 8 14 2 6 12 σ σ σ e ji i j ji i i C i r r q q F r r ∑ ≠ ⎟⎟ ⎟ ⎠ ⎞ ⎜⎜ ⎜ ⎝ ⎛ = 3 Precision (bit) Pipelines HW multipliers (% of usage) Block Ram (% of usage) Delay (ns) Speedup 35 4 176(53%) 214(65%) 11.1 12.2 13.2 18.0 22. 2 13.6 12.8 50.8× 40 4 264(80%) 251(77%) 46.4× 45 4 288(88%) 285(87%) 42.7× 51 4 288(88%) 317(97%) 31.3× 35 8 256(78%) 326(99%) 51.0× 51* 4 288(65%) 317(77%) 41.5× 35* 8 256(58%) 334(75%) 88.5× Forces: A typical force model has several components: bonded non H torsion angle bond total F F F F F F − + + + + = Precision, Resources, Accuracy: MD applications are usually run with double precision floating point. One advantage of implementing MD on FPGAs is that we can trade off hardware resources for simulation accuracy by varying the precision. By measuring the relationship among precision, time-step resolution, and simulation accuracy, we find that for precision beyond 40 bits, accuracy improves only very slowly. (See also [1].) Another measure of that the simulation accuracy is acceptable is that ΔEtotal/ ΔEkinetic < .05. For this, 30 bits are sufficient. Total Energy Fluctuation" @default.
• W2336528065 created "2016-06-24" @default.
• W2336528065 creator A5072905199 @default.
• W2336528065 date "2008-01-01" @default.
• W2336528065 modified "2023-09-26" @default.
• W2336528065 title "Fpga acceleration of molecular dynamics simulations" @default.
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• W2336528065 hasPublicationYear "2008" @default.
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