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)