Performance

Speed benchmarks

The simulation speed of ACEMD3 (version 3.2.0) was benchmarked with several systems at typical production conditions on different GPU devices. The GPU devices were mounted in Metrocubo machines and were operating under sustained load. The speed is measured in ns/day.

Device

Force field

System

DHFR

FactorIX

STMV

NVIDIA GeForce GTX 1080

AMBER

604

152

8.37

CHARMM

529

141

8.28

NVIDIA GeForce GTX 1080 Ti

AMBER

787

218

11.9

CHARMM

689

199

11.5

NVIDIA Tesla V100

AMBER

1045

407

25.4

CHARMM

973

364

25.0

NVIDIA GeForce RTX 2080 Ti

AMBER

997

306

17.1

CHARMM

915

286

17.3

The input files can be found in $CONDA_PREFIX/share/acemd3 after installing ACEMD3.

Simulation systems:
Simulation conditions:
  • Force field:
  • Electrostatic interactions:
    • Particle-mesh Ewald (PME)

    • Grid spacing: <1.0 Å

    • Real-space cutoff: 9.0 Å

  • van der Walls interactions:
    • Cutoff: 9.0 Å

    • Switch function: none for AMBER or 7.5 Å for CHARMM

  • Constraints:
    • Constrained hydrogen bonds

    • Rigid water

    • Constraint tolerance: 1.0e-6

  • Integrator and thermostat:
    • Multi-step integrator period: 2

    • Time step: 4.0 fs

    • Temperature: 298.15 K

    • Friction: 0.1 ps^-1

    • Hydrogen mass: 4.0 a.u

  • Output:
    • Trajectory period: 100 ps (25000 steps)