What is ACEMD#

ACEMD is a GPU-accelerated molecular-dynamics engine. Given a parameterised system and an input file, it can minimize the structure and propagate the integrator under your chosen thermostat, barostat, and restraints — covering minimization, equilibration, and production runs in the same engine. It does not build systems, prepare proteins, parameterise small molecules, or analyse trajectories; those tasks are handled upstream and downstream by HTMD and moleculekit.

What it does#

  • Integrator on the GPU. ACEMD is built on top of OpenMM, with custom tuning aimed at sustained single- and multi-GPU throughput.

  • Classical and machine-learned potentials. Classical CHARMM, AMBER, and OpenMM XML force fields are first-class. Neural-network potentials run either as a hybrid (NNP/MM — molecule on NNP, rest on MM) or pure NNP — see NNP and NNP/MM.

  • Ensembles. NVE, NVT (Langevin thermostat), and NPT (Monte Carlo barostat, isotropic / anisotropic / membrane).

  • Box shapes. Orthorhombic and triclinic (truncated octahedra, rhombic dodecahedra).

  • Output. XTC or DCD trajectories, optional velocity and force trajectories. CSV-formatted log with energies and timings.

  • Restart. Periodic checkpoints; resumable on the same GPU model.

Platform support#

  • NVIDIA GPUs via CUDA — the recommended target. Tested back to the Maxwell architecture; performance scales linearly with newer cards.

  • Other GPUs via OpenCL.

  • CPU for debugging — orders of magnitude slower than GPU, not for production.

ACEMD can be parallelised over multiple GPUs on a single host, though for typical system sizes splitting a single simulation across cards doesn’t speed it up — see Select GPU devices for when multi-GPU actually helps.

Integrations#

  • HTMD — system building and analysis pipelines.

  • PLUMED — enhanced sampling (metadynamics, steered MD) and complex restraints. See Run with PLUMED.

  • moleculekit — reading, writing, and analysing trajectories.

What it doesn’t do#

  • No system preparation (protonation, mutation, solvation) — use moleculekit’s systemPrepare() or HTMD.

  • No parameterisation of non-canonical chemistry — small molecules, stapled peptides, non-canonical amino acids, modified residues. Use HTMD, which wraps OpenFF, GAFF/Antechamber, CGenFF, and related generators in a unified parameterisation pipeline, then bring the topology to ACEMD.

  • No trajectory analysis — once the run finishes, hand output.xtc to moleculekit / HTMD / MDAnalysis / your tool of choice.

ACEMD is widely used in academic and industrial MD research; the original engine paper has been cited over 700 times.

See also#