Performance

Speed benchmarks

The simulation speed of ACEMD (version 3.4.0) was benchmarked against 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	621	136	7.01
	CHARMM	555	134	8.37
NVIDIA GeForce GTX 1080 Ti	AMBER	762	202	9.89
	CHARMM	672	190	11.4
NVIDIA GeForce RTX 2080 Ti	AMBER	1040	313	15.4
	CHARMM	979	296	17.0
NVIDIA GeForce RTX 3090	AMBER	1308	434	22.4
	CHARMM	1258	416	25.1

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

Simulation systems:

• DHFR (Dihydrofolate reductase)

  • Number of atoms: 23,558

  • Box size: 62.23 Å ✕ 62.23 Å ✕ 62.23 Å

• FactorIX (Factor IX)

  • Number of atoms: 90,906

  • Box size: 142.09 Å ✕ 83.34 Å ✕ 78.68 Å

• STMV (Satellite tobacco mosaic virus)

  • Number of atoms: 1,067,095

  • Box size: 221.2 Å ✕ 223.2 Å ✕ 224.5 Å

Simulation conditions:

• Force field:

  • AMBER ff99SB or CHARMM 36

  • TIP3P

• 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)