NVIDIA Ampere GPU Benchmarks for AMBER 20

GPU Benchmark Overview

AMBER 20 GPU Benchmark: JAC Production NVE 4fs

AMBER 20 GPU Benchmark: JAC Production NPT 4fs

AMBER 20 GPU Benchmark: JAC Production NVE 2fs

AMBER 20 GPU Benchmark: JAC Production NPT 2fs

AMBER 20 GPU Benchmark: FactorIX Production NVE and NPT 2fs

AMBER 20 GPU Benchmark: Cellulose Production NVE 2fs

AMBER 20 GPU Benchmark: Cellulose Production NPT 2fs

AMBER 20 GPU Benchmark: STMV Production NPT 4fs

AMBER 20 GPU Benchmark: TRPCage GB 2fs

AMBER GPU Benchmark: Myoglobin GB 2fs

AMBER GPU Benchmark: Nucleosome GB 2fs

Note about AMBER 20 Benchmarks (From Dave Cerutti)

We take as benchmarks four periodic systems spanning a range of system sizes and compositions. The smallest Dihydrofolate Reductase (DHFR) case is a 159-residue protein in water, weighing in at 23,588 atoms. Next, from the human blood clotting system, Factor IX is a 379-residue protein also in a box of water, total 90,906 atoms. The larger cellulose system, 408,609 atoms, has a greater content of macromolecules in it: the repeating sugar polymer constitutes roughly a sixth of the atoms in the system. Finally, the very large simulation of satellite tobacco mosaic virus (STMV), a gargantuan 1,067,095 atom system, also has an appreciable macromolecule content, but is otherwise another collection of proteins in water. (source http://ambermd.org/GPUPerformance.php)

What is AMBER Molecular Dynamics Package?

If you’re not familiar with AMBER it refers to ‘Assisted Model Building with Energy Refinement‘, a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman’s group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields, and is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Adrian Roitberg at University of Florida, Ken Merz at Michigan State University, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.

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