The Toolbox for Molecular Dynamics
Software to cover every step of the simulation process.
The platform includes:
- ACEMD: Acellera’s engine for running molecular dynamics simulations. Over 750 citations.
- HTMD: Build your system, simulate it, and analyze your trajectories with a handful of Python lines.
- Parameterize: Obtain accurate force-field parameters for your small molecules.
- Metrocubo (optional): Acellera’s GPU-based supercomputer of desktop size. Specially designed to run MD, with latest ACEMD version installed.
“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.
Molecular Dynamics Simulations and Computer-Aided Drug Discovery (pp. 1–30). https://doi.org/10.1007/7653_2015_41
ACEMD
As fast as possible Molecular Dynamics
- Speed: Designed and engineered with simulation speed in mind.
- Suited for drug discovery: It has been used to study protein-ligand binding, conduct small virtual screening campaigns or sample structural changes in large proteins.
- PLUMED integration: Run metadynamics with its PLUMED plugin.
HTMD
A powerful, open-source Python library for computational chemistry and structural biology.
- Manipulate molecules: Perform all kinds of operations to your molecules with a couple of functions.
- Run molecular dynamics: Prepare, build, run and analyze simulations through its integration with ACEMD.
- Benefit from our experience: Documentation and tutorials available at software.acellera.com. Full source code available at our Github repo.
Parameterize
Adding small molecules to the mix
While forcefield parameters are readily available for proteins, parameters for small molecules must be computed. Parameterize is Acellera’s force field parameterization tool, which works in 4 easy steps:
- Input your molecule as a .mol2 or .sdf file.
- Choose between forcefields.
- Choose between quantum, machine-learning or heuristic-based rules to compute parameters.
- Done! Get your results in the form of a .frcmod file.
Extensive documentation can be found here, while an online GUI is available at PlayMolecule.
TorchMD
The framework for differentiable chemistry and biology
TorchMD provides a simple to use API for performing molecular dynamics using PyTorch. This enables researchers to more rapidly do research in force-field development as well as integrate seamlessly neural network potentials (NNPs) into the dynamics, with the simplicity and power of PyTorch.
TorchMD has already been shown to be capable of:
- Deriving force field parameters from a short MD trajectory.
- Creating a coarse-grained model for an arbitrary protein using NNPs.
Metrocubo
The desktop-size supercomputer
Loaded with modern GPUs and the latest version of ACEMD, Metrocubo can run at full GPU loads for extended periods of time uninterrupted. Metrocubo hardware is available for purchase worldwide.
