GROMACS

GROMACS is the local molecular-dynamics engine used for planned h01 Phase 9 endpoint free-energy and PMF tracks.

Local install

• Version: GROMACS 2026.1-Homebrew
• Executable: /opt/homebrew/bin/gmx
• GPU support: disabled in the Homebrew build
• SIMD: ARM_NEON_ASIMD
• Use in h01: topology / trajectory handling and possible CPU-only smoke runs, not long production MD on Apple Silicon.

Commands

gmx --version
gmx trjconv
gmx make_ndx
gmx wham

Output formats

• Structure: .gro, .pdb
• Trajectory: .xtc, .trr
• Energy: .edr, .xvg
• Topology: .top, .itp, .ndx

Apple Silicon note

The installed Homebrew build is CPU-only. For multi-hour h01 production MD, use OpenMM Metal/OpenCL or a remote GPU GROMACS build. CPU-only GROMACS is acceptable for short preprocessing and smoke-level trajectory manipulation.

License / source

• License: LGPL
• Source: https://www.gromacs.org/

Connections

• [applies] STRC h01 Phase 9 Orthogonal Cross-Checks Plan 2026-04-27
• [see-also] gmx_MMPBSA
• [see-also] AmberTools
• [part-of] STRC Tools
• [part-of] Tools index