Benchmark: OpenMM on Dihydrofolate Reductase (DHFR)


Benchmark Settings

OpenMM was benchmarked on the dihydrofolate reductase (DHFR) models taken from the Joint Amber/Charmm benchmark. This is a 159 residue protein with 2489 atoms. The version used for explicit solvent simulations included 7023 TIP3P water molecules, giving a total of 23,558 atoms. All simulations used the AMBER99SB force field and a Langevin integrator, and were run with OpenMM 7.3.

Treatment of Solvent

Three different methods were used to calculate the effect of solvent:

  1. Implicit: Solvent was represented with an OBC-GBSA implicit solvent model. Long range interactions were cut off at 2 nm.

  2. Explicit-RF: Solvent was modeled explicitly. Long range interactions were cut off at 1 nm using the reaction field method.

  3. Explicit-PME: Solvent was modeled explicitly. Long range interactions were calculated using Particle Mesh Ewald. The Ewald error tolerance was set to 0.0005, and the direct space cutoff was chosen to optimize performance (0.9 nm for the GPU simulations, 0.8 nm for the CPU simulations).

Time Step

Two step sizes were used for the simulations:

  1. 2 fs For these simulations, the lengths of bonds involving hydrogen were constrained.

  2. 5 fs For these simulations, the lengths of all bonds were constrained. In addition, mass repartitioning was used to increase the mass of hydrogen atoms to 4 amu.

Water molecules were fully rigid in all cases, and the constraint error tolerance was set to 0.00001.

Platforms

Simulations were run using the following platforms and hardware:

  1. CUDA platform on an NVIDIA Titan X Pascal GPU.
  2. CUDA platform on an NVIDIA Titan V GPU.
  3. OpenCL platform on NVIDIA Titan X Pascal GPU.
  4. OpenCL platform on NVIDIA Titan V GPU.
  5. OpenCL platform on an AMD Radeon RX Vega 64 GPU.
  6. CPU platform on a 4 core 4.3 GHz Intel Core i7-7740X CPU.


Results

Performance is measured in ns/day.

CUDA Titan X

CUDA Titan V

OpenCL Titan X

OpenCL Titan V

OpenCL Radeon

CPU

Implicit, 2 fs

912

903

688

742

321

9.2

Implicit, 5 fs

1500

1299

778

1003

407

22.4

Explicit-RF, 2 fs

612

623

514

580

281

19.2

Explicit-RF, 5 fs

1093

980

680

835

373

43.0

Explicit-PME, 2 fs

421

375

307

299

140

11.6

Explicit-PME, 5 fs

819

716

482

585

262

26.9


BenchmarkOpenMMDHFR (last edited 2018-12-19 19:22:41 by peastman)