A free GROMACS benchmark set
Input files for GROMACS performance evaluations
Benchmark set description
These benchmarks are typical simulation systems from our research projects and cover a wide range of system sizes from 6k to 12M atoms. Some technical specifications of the benchmark input files are listed in the PDF file given above. With the exception ofbenchPEP-h, all standard benchmarks use all bonds constraints, which means that the update step has to be done on the CPU. On nodes with powerful GPUs however, GROMACS performance is often highest when all work in the time step is done on the GPU, which is possible with the benchPEP-h benchmark (using the command line switches -pme gpu -update gpu -bonded gpu).
Standard MD benchmarks
- benchMEM (82k atoms, protein in membrane surrounded by water, 2 fs time step) 1.65 MB
- benchPEP (12 M atoms, peptides in water, 2 fs time step, all bonds constrained) 212.98 MB
- benchPEP-h (12 M atoms, peptides in water, 2 fs time step, h-bonds constrained) 213.05 MB
- benchRIB (2 M atoms, ribosome in water, 4 fs time step) 54.81 MB
- dobenchs 1.83 kB
- extract 1.28 kB
Binding affinity study benchmarks
- CMET (67 k atoms), protein+ligand, equilibration 1.35 MB
- CMET (67 k atoms), protein+ligand, TI 1.35 MB
- HIF2A (36 k atoms), protein+ligand, equilibration 701.91 kB
- HIF2A (36 k atoms), protein+ligand, TI 700.56 kB
- CMET (6 k atoms), ligand, equilibration 119.51 kB
- CMET (6 k atoms), ligand, TI 119.57 kB
- SHP2 (107 k atoms), protein+ligand, equilibration 2.19 MB
- SHP2 (107 k atoms), protein+ligand, TI 2.19 MB
Other free energy benchmarks
- benchBFC (binding, fep, nstcalcenergy=100) 868.78 kB
- benchBFI (binding, fep, nstcalcenergy=1) 868.78 kB
- benchBNC (binding, no free energy, nstcalcenergy=100) 863.0 kB
- benchBNI (binding, no free energy, nstcalcenergy=1) 863.0 kB
- benchBTC (binding, TI, nstcalcenergy=100) 868.67 kB
- benchBTI (binding, TI, nstcalcenergy=1) 868.68 kB
- benchSFC (solvation, fep, nstcalcenergy=100) 70.72 kB
- benchSFI (solvation, fep, nstcalcenergy=1) 70.72 kB
- benchSNC (solvation, no free energy, nstcalcenergy=100) 65.05 kB
- benchSNI (solvation, no free energy, nstcalcenergy=1) 65.05 kB
- benchSTC (solvation, TI, nstcalcenergy=100) 70.6 kB
- benchSTI (solvation, TI, nstcalcenergy=1) 70.6 kB
License
The GROMACS input .tpr files are licensed under the
CC-BY 4.0
Creative Commons Attribution 4.0 International license.
Please attribute to:
Dept. of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, https://www.mpinat.mpg.de/grubmueller/bench.
The benchmark set builds upon simulation systems listed in the "References" section. Parts of it have been used in the publications listed in the "Publications" section.
Publications
GROMACS in the cloud: A global supercomputer to speed up alchemical drug design. Journal of Chemical Information and Modeling 62 (7), pp. 1691 - 1711 (2022)
More bang for your buck: Improved use of GPU nodes for GROMACS 2018. Journal of Computational Chemistry 40 (27), pp. 2418 - 2431 (2019)
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. Journal of Computational Chemistry 36 (26), pp. 1990 - 2008 (2015)
Tackling exascale software challenges in molecular dynamics simulations with GROMACS. In: Solving Software Challenges for Exascale: International Conference on Exascale Applications and Software, EASC 2014, Stockholm, Sweden, April 2-3, 2014, Revised Selected Papers, pp. 3 - 27 (Eds. Markidis, S.; Laure, E.). Springer, Cham (2015)
Scaling of the GROMACS 4.6 molecular dynamics code on SuperMUC. In: Parallel Computing: Accelerating Computational Science and Engineering (CSE), pp. 722 - 730 (Eds. Bader, M.; Bode, A.; Bungartz, H. J.). IOS Press, Amsterdam (2014)
GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 4 (3), pp. 435 - 447 (2008)
References
Original publications of the benchmark simulation systems
Water permeation across biological membranes: Mechanism and dynamics of Aquaporin-1 and GlpF. Science 294, pp. 2353 - 2357 (2001)
Energy barriers and driving forces in tRNA translocation through the ribosome. Nature Structural and Molecular Biology 20 (12), pp. 1390 - 1396 (2013)
Driving forces and structural determinants of steric zipper peptide oligomer formation elucidated by atomistic simulations. Journal of Molecular Biology 421 (2-3), pp. 390 - 416 (2012)