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 7.1.

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. OpenCL platform on NVIDIA Titan X Pascal GPU.
  3. CPU platform using 16 threads on a 2.3 GHz Intel Xeon E5-2697 v4 CPU.


Results

Performance is measured in ns/day.

CUDA

OpenCL

CPU

Implict, 2 fs

863

665

19.8

Implict, 5 fs

1386

816

44.1

Explict-RF, 2 fs

607

486

21.0

Explict-RF, 5 fs

1047

689

43.6

Explict-PME, 2 fs

384

288

15.6

Explict-PME, 5 fs

762

430

34.8


BenchmarkOpenMMDHFR (last edited 2017-02-08 22:16:09 by peastman)