Table des matières
Benchmarks for Gromacs on Jean Zay
Description of benchmark 6vnx
System
The system is a protein in a box of water:
- Number of atoms:
- Total = 932,310
- Solvent = 887,139
- Protein = 45,156
- Counter ions = 15
- Box:
- cubic 21.14 Å
Simulation
The simulation is run with Gromacs 2020.1 and has the following setup:
- Type of simulation: molecular dynamics
- Ensemble: NVT
- Number of steps: 500,000
- Timestep : 2 fs
- Long range electrostatic : Particle Mesh Ewald
- PME cutoff: 1.2 Å
- van der Waals cutoff: 1.1 Å
- cutoff-scheme: Verlet
- Temperature coupling: V-rescale
- Constraints: LINCS on H-bonds