AMBER 20 GPU Benchmarks for Molecular Dynamics

 **10/20/2020 UPDATED with NVIDIA RTX 3080**

The following Amber 20 Benchmarks were performed on an Exxact AMBER Certified MD System using the following GPUs NVIDIA GeForce RTX 3090, NVIDIA A100 (PCIe), NVIDIA Quadro RTX 6000, and NVIDIA GeForce RTX 2080 Ti using the AMBER 20 Benchmark Suite.

All benchmarks were performed using a single GPU configuration using Amber 20 Update 6 & AmberTools 20 Update 9. NVIDIA CUDA 11.1 was also used for these benchmarks.

Quick AMBER GPU Benchmark takeaways

  • Ampere GPUs (RTX 3090, RTX 3080 & A100) outperformed all Turing models (2080 Ti & RTX 6000) across the board.
  • For the larger simulations, such as STMV Production NPT 4fs, the A100 outperformed all others.
  • For smaller simulations the RTX 3090 and RTX 3080 showed excellent performance, and in some cases on par with the A100.

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GPU Benchmark Overview

Benchmark RTX2080TI RTX6000 A100 PCIe RTX3080 RTX3090
JAC Production NVE 4fs 970.51 1034.88 1199.22 1101.24 1196.5
JAC Production NPT 4fs 940.61 1004.03 1194.5 1086.21 1157.76
JAC Production NVE 2fs 510.21 540.17 611.08 585.81 632.19
JAC Production NPT 2fs 488.36 515.86 610.09 557.6 595.28
FactorIX Production NVE 2fs 205.92 217.25 271.36 234.58 264.78
FactorIX Production NPT 2fs 189.99 206 252.87 217.5 248.65
Cellulose Production NVE 2fs 43.89 47.41 85.23 53.44 63.23
Cellulose Production NPT 2fs 40.77 45.24 77.98 49.69 58.3
STMV Production NPT 4fs 25.21 28.49 52.02 32.18 38.65
TRPCage GB 2fs 1151.74 1189.25 1040.61 1332.27 1225.53
Myoglobin GB 2fs 505.93 600.83 661.22 619.67 621.73
Nucleosome GB 2fs 15.22 16.81 29.66 17.72 21.08


AMBER 20 GPU Benchmark: JAC Production NVE 4fs

RTX 3080 Benchmark

AMBER 20 GPU Benchmark: JAC Production NPT 4fsAMBER 20 HPC Benchmark GPU

AMBER 20 GPU Benchmark: JAC Production NVE 2fsAMBER 20 HPC Benchmark RTX 3080

AMBER 20 GPU Benchmark: JAC Production NPT 2fsAMBER 20 HPC Benchmark

AMBER 20 GPU Benchmark: FactorIX Production NVE 2fs


AMBER 20 GPU Benchmark: FactorIX Production NPT 2fs


AMBER 20 GPU Benchmark: Cellulose Production NVE 2fs


AMBER 20 GPU Benchmark: Cellulose Production NPT 2fsAMBER HPC Benchmark

AMBER 20 GPU Benchmark: STMV Production NPT 4fsRTX 3080 Benchmark GPUs

AMBER 20 GPU Benchmark: TRPCage GB 2fsRTX 3080 Benchmark GPUs HPC

AMBER GPU Benchmark: Myoglobin GB 2fsRTX 3080 Benchmark GPU

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

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. (1)

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