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NEB.pdf (15.21 MB)
A Fast Implementation of the Nudged Elastic Band Method in AMBER
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We present a fast implementation of the nudged elastic band (NEB) method into the particle mesh Ewald molecular dynamics (pmemd) module of the Amber software package both for central processing units (CPU) and graphics processing units (GPU). The accuracy of the new implementation has been validated for three cases: a conformational change of alanine dipeptide, the α-helix to ß-sheet transition in polyalanine, and a large conformational transition in human 8-oxoguanine–DNA glycosylase with DNA complex (OGG1–DNA). Timing benchmark tests were performed on the explicitly solvated OGG1–DNA system containing ~50k atoms. The GPU-optimized implementation of NEB achieves more than two orders of magnitude speedup compared to the previous CPU implementation performed with a two-core CPU processor. The speed and scalable features of this implementation will enable NEB applications on larger and more complex systems.