Benchmark
Benchmark of GENESIS 2.0 beta / 1.6 on FUGAKU
- CPU: A64FX (2.0 GHz)
- Compile conditions: Fujitsu compiler 4.3.0a tcsds-1.2.28 / Single precision
- Integrator: Velocity Verlet (VV) and Multiple Time Step (MTS)
- Time step: 2 fs (VV), 2.5 fs / 5.0 fs (MTS, ver. 1.6), 3.5 fs / 7.0 fs (MTS, ver. 2.0)
DHFR (27,346 atoms)
NVT
- Force field: AMBER
- switch, cutoff, pairlist = 8, 8, 9.5 Å
NPT
- Force field: AMBER
- switch, cutoff, pairlist = 8, 8, 9.5 Å
ApoA1 (92,224 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
UUN (216,726 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
Crowding System (1,578,958 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
Huge Crowding System
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
Benchmark of GENESIS 2.0 beta on CPU+GPU cluster
- CPU: Intel Xeon Gold 6142 (2.6 GHz)
- GPU: GeForce GTX 1080Ti
- Compile conditions: Intel MPI ver. 19.1 / Intel compiler ver. 19.1 / Single precision
- Integrator: Velocity Verlet (VV) and Multiple Time Step (MTS)
- Time step: 2 fs (VV), 3.5 fs / 7.0 fs (MTS)
DHFR (27,346 atoms)
NVT
- Force field: AMBER
- switch, cutoff, pairlist = 8, 8, 9.5 Å
NPT
- Force field: AMBER
- switch, cutoff, pairlist = 8, 8, 9.5 Å
ApoA1 (92,224 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
UUN (216,726 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
Crowding System (1,578,958 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
Benchmark of GENESIS 1.6 on CPU+GPU cluster
- CPU: Intel Xeon Gold 6142 (2.6 GHz)
- GPU: GeForce GTX 1080Ti
- Compile conditions: Intel MPI ver. 19.1 / Intel compiler ver. 19.1 / Mixed precision
- Integrator: Velocity Verlet (VV) and Multiple Time Step (MTS)
- Time step: 2 fs (VV), 2.5 fs / 5.0 fs (MTS)
DHFR (27,346 atoms)
NVT
- Force field: AMBER
- switch, cutoff, pairlist = 8, 8, 9.5 Å
NPT
- Force field: AMBER
- switch, cutoff, pairlist = 8, 8, 9.5 Å
ApoA1 (92,224 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
UUN (216,726 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
Crowding System (1,578,958 atoms)
NVT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
NPT
- Force field: CHARMM
- switch, cutoff, pairlist = 10, 12, 13.5 Å
Input and control files of the benchmark
Get the input files of GENESIS benchmark from our GitHub repository.