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 |
||
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 |
The input files can be found in $CONDA_PREFIX/share/acemd3
after installing ACEMD.
Number of atoms: 23,558
Box size: 62.23 Å ✕ 62.23 Å ✕ 62.23 Å
Number of atoms: 90,906
Box size: 142.09 Å ✕ 83.34 Å ✕ 78.68 Å
Number of atoms: 1,067,095
Box size: 221.2 Å ✕ 223.2 Å ✕ 224.5 Å
Particle-mesh Ewald (PME)
Grid spacing: <1.0 Å
Real-space cutoff: 9.0 Å
Cutoff: 9.0 Å
Switch function: none for AMBER or 7.5 Å for CHARMM
Constrained hydrogen bonds
Rigid water
Constraint tolerance: 1.0e-6
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
Trajectory period: 100 ps (25000 steps)