Molecular Dynamics made simple
What is it?
ACEMD Platform is a complete and fast solution package, designed to run and analyze your molecular dynamics (MD) simulations. It includes both ACEMD and HTMD packages. ACEMD is the MD engine that runs the simulation, while HTMD is a Python package that you can use to create systems, prepare them and, once ACEMD has finished simulating those systems, analyze their trajectories.
ACEMD: A GPU-optimized MD engine
ACEMD is a high-performance molecular dynamics code to simulate biomolecular systems. It was specifically designed to run on Nvidia GPUs, which provides a dramatic increase in speed compared with CPU-based engines: one GPU card can outperform up to hundreds of CPU units running in parallel . ACEMD and NAMD both use very similar commands, input and output files. ACEMD has the following features and capabilities:
- Compatible with ff99SB and charmm36 force fields
- Supported input file formats: PDB, PSF, PRMTOP, NAMD Bincoor
- Output file formats: PDB, NAMD Bincoor, XTC
- Thermostat Langevin
- Constraints and restraints M-SHAKE with RATTLE correction, positional harmonic restraints
- Total integration with HTMD
HTMD: A Python package to manipulate molecules
HTMD is a unique, molecular-specific, programmable environment to prepare, handle, simulate, visualize and analyze molecular systems. HTMD is written in Python, in order to allow scientists to easily extend it to their needs and use it in combination with their favorite Python libraries. With HTMD, it is possible to perform very complex protocols with just a few lines of code. With a single script, you can plan an entire computational experiment, starting with the preparation of the molecular structures and finishing with the analysis of its simulation, including calculating Markov state models, kinetic rates, affinities and binding pathways.