Journal
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Volume 15, Issue 8, Pages 4699-4707Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.9b00329
Keywords
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Funding
- National Science Foundation [OCI-0725070, ACI-1238993, ACI-1548562]
- state of Illinois
- National Institutes of Health [R01 GM107104]
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We present a fast implementation of the nudged elastic band (NEB) method into the particle mesh Ewald molecular dynamics module of the Amber software package for both 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 alpha-helix to beta-sheet transition in polyalanine, and a large conformational transition in the human 8-oxoguanine-DNA glycosylase with DNA complex (OGG1-DNA). Timing benchmark tests were performed on the explicitly solvated OGG1-DNA system containing similar to 50 000 atoms. The GPU-optimized implementation of NEB achieves a more than two orders of magnitude speedup compared with 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.
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