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 computer (link to metrocubo).
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 (link to d3r dopamine paper), or protein folding, among others. Check the success stories tab for more examples.
ACEMD can run for free on one 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.
- Videos, tutorials and recipes can be found here.
- Furthermore, if you need our support to install ACEMD in your computer or cluster, or to develop novel protocols, you can contact us here.
The setup process is super easy through conda:
conda install -c conda-forge -c acellera acemd3
Single GPU setup
Free-of-charge for both academic and commercial use.
Requires a license purchase from Acellera. More details here.
successful applications of ACEMD
(GPCR paper details)
(paper 2 description)
“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