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Until the development of modern GPUs, Molecular Dynamics simulations were limited to the nanosecond scale. Given that most biochemical processes (protein folding, ligand binding etc.) happen in the microsecond to millisecond timescales, MD simulations were of limited applicability. However, with the emergence of GPUs and the development of ACEMD, we can now simulate trajectories of several microseconds or even milliseconds for small and medium proteins, like kinases or ion channels, using a desktop-size supercomputer.

Since the appearance of ACEMD, multiple academic and industrial groups have used it to obtain structural insights in real-world applications, like binding mode prediction, or protein folding, among others. Check the success stories section below for more examples.

ACEMD can run for free on a single GPU, while a license is required to run on multiple GPUs. Contact us to request a license or learn more.

  • NVIDIA GPU support (Maxwell architecture or later)
  • Other GPU support via OpenCL
  • Parallelization over GPUs
  • CPU support (for debugging)
  • AMBER and CHARMM force fields
  • TIP3P water model
  • Efficient electrostatic interactions with PME
  • Efficient van der Waals interactions with the pair list and switching function
  • Efficient bond constraints and rigid water molecules
  • Hydrogen mass repartitioning
  • Position restraints of individual atoms and groups
  • Structure minimization
  • Multi-step integrator
  • Ensembles: NVE, NVT, and NPT
  • Langevin thermostat
  • Monte Carlo barostat (isotropic and anisotropic simulation boxes)
  • Trajectory in XTC or DCD formats
  • Restartable simulations
  • Integration with HTMD and  PLUMED
  • Extensive, up-to-date documentation can be found here.
  • Contact us for installation support for ACEMD on your computer or cluster, or to develop novel protocols.
You can see more details regarding benchmark data here.

Testimonials

ACEMD allows to perform state-of-the-art molecular dynamics simulations on your own desktop or server equipped with GPUs. It is user-friendly and through its simplicity for standard simulations, it can be customized through the use of a plugin module to be written in C or in combination with PLUMED.

“ACEMD is without any doubt a versatile program that exploit the full potential of MD simulations, using cost-effective hardware solutions, that can be adapted to every Molecular Modeling laboratory needs.”

“Acellera and ACEMD afforded us a straightforward new tool based on its amazing MD engine performance capable to exploit fully the latest GPU hardwares. It can be easily plugged to extra codes for a maximal versatility and no doubts remains on its usefulness for an atomic scale interpretation of biomolecular NMR data and its specific spectroscopic time-scales.”

“ACEMD is an admirable molecular dynamics tool that clearly holds its promises.”

“ACEMD has provided a significant boost in performance, even a single GPU card out performs several hundred CPU-cores. With 10 cards we can easily generate microsecond level sampling in a few days.”

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Installing ACEMD

ACEMD can be easily installed using the Conda Package Manager:

conda install -c conda-forge -c acellera acemd3
gpu-64 1

Single GPU setup

Free-of-charge for both academic and commercial use.

gpu-64 N

Multi-GPU Setup

License purchase from Acellera required. Contact us for details.

success stories

successful applications of ACEMD

pfizer-collaboration

Sampling new binding modes in cryptic pockets that agree with mutagenesis studies using ACEMD.

GPCR-1

Transitioning a GPCR from inactive state to active state using unbiased, all atom molecular dynamics simulations with ACEMD.

“Until and unless other suites emerge that are as GPU-enabled, the ideal simulation technology at present is ACEMD on GPUs.”

Godwin, R. C., Melvin, R., & Salsbury, F. R. (2015)

Molecular Dynamics Simulations and Computer-Aided Drug Discovery (pp. 1–30). https://doi.org/10.1007/7653_2015_41

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