What is it?
ACEMD Platform is a complete and fast solution package, specially 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 Amber and CHARMM 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.
MOLECULAR DYNAMICS SIMULATION APPS
Acellera has developed a set of applications to prepare and analyze MD simulations, that run on our drug discovery platform, PlayMolecule:
- ProteinPrepare - To prepare proteins for molecular dynamics simulations by titrating and protonating the protein at a desired pH and by optimizing the H-bond network.
- SystemBuilder - To build globular and membrane protein-ligand systems ready to run molecular dynamics simulations
- MembraneBuilder - To build complex lipid membranes including POPC, POPE and cholesterol for molecular dynamics simulations
- PlexView - To create aesthetic 2D diagrams of protein-ligand interactions including hydrogen-bonds and pi-pi stacking
- AdaptiveSampling - To explore the protein conformational space or protein-ligand interaction space by running MD simulations along the metric of your choice
- Parameterize - For fast and accurate molecular force field parameterization of drug-like molecules. Generate parameters in the AMBER-compatible format