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 all supported directly. Neural-network potentials run either as a hybrid (NNP/MM, with the molecule on the NNP and the rest on MM) or as 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 and not meant 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#