GROMACS vs NAMD: Single-GPU Speed vs Multi-GPU Scalability

By BioDockify Computational Research Team · August 9, 2026 · Comparison

Technical comparison of GROMACS and NAMD molecular dynamics engines. Performance benchmarks, scalability, and when to choose each for protein simulation.

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

Key References

• Abraham, M.J. et al. GROMACS. SoftwareX 1-2, 19-25 (2015).
• Phillips, J.C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).

Scope & Limitations

NAMD requires more setup for GPU acceleration GROMACS has better single-GPU optimization Performance depends on system size and hardware