Performance

Speed benchmarks

The simulation speed of ACEMD was benchmarked against several systems at typical production conditions on different GPU devices. The GPU devices were operating under sustained load. The speed is measured in ns/day.

Device	Force field	System
		DHFR	FactorIX	STMV
NVIDIA GeForce GTX 1080	AMBER	500	120	6.86
	CHARMM	467	116	7.48
NVIDIA GeForce GTX 1080 Ti	AMBER	623	180	9.94
	CHARMM	600	163	10.7
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
NVIDIA GeForce RTX 4090	AMBER	1810	777	59.2
	CHARMM	1772	711	58.4

The input files for the benchmark systems can be downloaded here

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:

  • 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)