acemd 4.1.3

ACEMD is the next generation molecular dynamic simulation software

ACEMD

ACEMD is the next generation molecular dynamics (MD) simulation software designed for high performance and ease of use.

Features

• High Performance: Optimized for NVIDIA GPUs with CUDA support
• Multiple Force Fields: Support for AMBER, CHARMM, and OpenMM XML force fields
• Small Molecule Support: Automated parameterization using GAFF, OpenFF, and Espaloma force fields
• Neural Network Potentials: Integration with TorchMD-NET, ANI, and other ML potentials
• Flexible I/O: Multiple trajectory formats
• Python API: Full control through Python scripting
• Advanced Sampling: Support for metadynamics, steered MD, and custom forces

Installation

Prerequisites

• Python 3.10 or higher
• NVIDIA GPU with CUDA support

Install with pip (recommended)

The simplest way to install ACEMD is using pip:

# GPU version with CUDA 12
pip install "acemd[cu12]"

# GPU version with CUDA 13
pip install "acemd[cu13]"

# With additional neural network potential support
pip install "acemd[nnp-cu12]" --extra-index-url https://download.pytorch.org/whl/cu126

# With additional OpenFF support
pip install "acemd[nnp-cu12,openff]" --extra-index-url https://download.pytorch.org/whl/cu126

Install with conda/mamba

For conda users, ACEMD is available from the acellera channel:

conda install acemd cuda-version=12 -c acellera -c conda-forge

Quick Start

Command Line Usage

Create an input configuration file input.yaml:

# Example with AMBER files
structure: system.prmtop
coordinates: system.pdb
thermostat: true
thermostattemperature: 300
timestep: 4
run: 4ns

# Example with OpenMM XML force fields
# structure: system.pdb
# parameters: [amber14-all.xml, amber14/tip3pfb.xml]

Run the simulation:

# You can omit the --input argument if running in a directory with an input.yaml available
acemd --input input.yaml

Python API

from acemd import acemd

# Run simulation from a directory containing input file
acemd('/path/to/simulation/directory')

# Example of creating input file programmatically
import yaml

input_dict = {
    'structure': 'system.prmtop',
    'coordinates': 'system.pdb',
    'thermostat': True,
    'thermostattemperature': 300,
    'timestep': 4,
    'run': '4ns'
}

with open('input.yaml', 'w') as f:
    yaml.dump(input_dict, f)

acemd('.')

Small Molecule Simulations

ACEMD can also automatically parameterize small molecules:

structure: protein_ligand.pdb
parameters: [amber14-all.xml, amber14/tip3pfb.xml]
molecules:
  smiles:
    LIG: "CC(=O)NC1=CC=C(C=C1)O"
  forcefield: gaff-2.2.20
  charge_model: am1bcc
thermostat: true
thermostattemperature: 300
timestep: 4
run: 4ns

Documentation

Full documentation is available at https://software.acellera.com/acemd

Key Topics

• Installation Guide
• Manual
• Tutorial

License

ACEMD is commercial software. For licensing information, please contact [e-mail].

Non-commercial usage is free.

Citation

If you use ACEMD in your research, please cite:

@article{acemd2009,
  title={ACEMD: Accelerating biomolecular dynamics in the microsecond time scale},
  author={MJ Harvey, G Giupponi, G De Fabritiis},
  journal={Journal of Chemical Theory and Computation},
  year={2009}
}

Support

• Documentation: https://software.acellera.com/acemd
• Support: [e-mail]
• Licenses: [e-mail]