MD Simulation Without a GPU: Every Practical Option, Compared

By BioDockify Computational Research Team · October 11, 2026 · MD Fundamentals

You do not need a GPU workstation to run molecular dynamics: CPU-only reality and benchmarks, cloud GPU by the hour, browser platforms, academic HPC, and scope-reduction strategies - compared by cost, system size and practicality.

Read the complete article with tables, code and references on BioDockify.

Key References

• Abraham, M.J. et al. GROMACS: High performance molecular simulations through multi-level parallelism. SoftwareX 1-2, 19-25 (2015). DOI: 10.1016/j.softx.2015.06.001
• Eastman, P. et al. OpenMM 7: Rapid development of software for molecular dynamics. PLoS Comput. Biol. 13, e1005659 (2017). DOI: 10.1371/journal.pcbi.1005659
• Kasson, P.M. et al. Large-scale molecular dynamics on cloud infrastructure. J. Phys. Chem. B 113, 13798-13802 (2009).

Scope & Limitations

Exact ns/day depends on system, software and hardware generation - treat numbers as planning ranges, not guarantees Scope-reduction options (implicit solvent, smaller boxes) change the physics being sampled; justify them or do not use them