Performance

Speed benchmarks

The simulation speed of ACEMD3 (version 3.1.0) was benchmarked with two 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 STMV
NVIDIA GeForce GTX 1080 AMBER 504 7.02
CHARMM 420 7.05
NVIDIA GeForce GTX 1080 Ti AMBER 690 10.2
CHARMM 564 10.0
NVIDIA Titan V AMBER 761 18.5
CHARMM 686 18.5
NVIDIA GeForce RTX 2080 Ti AMBER 930 16.3
CHARMM 802 15.8

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:
    • Langevin
    • 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)