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 |
||
AMBER |
621 |
136 |
7.01 |
|
CHARMM |
555 |
134 |
8.37 |
|
AMBER |
762 |
202 |
9.89 |
|
CHARMM |
672 |
190 |
11.4 |
|
AMBER |
1040 |
313 |
15.4 |
|
CHARMM |
979 |
296 |
17.0 |
|
AMBER |
1308 |
434 |
22.4 |
|
CHARMM |
1258 |
416 |
25.1 |
|
AMBER |
2144 |
822 |
58.2 |
|
CHARMM |
2051 |
791 |
56.8 |
The input files can be found in $CONDA_PREFIX/share/acemd
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:
- 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)