Acellera's Blog

AceCloud – Simplified, Limitless Molecular Dynamics Simulations on the Cloud

by Matt Harvey, CTO

Physics-based computer simulation offers a tremendously powerful way to gain insight into the behavior of a wide variety of complex systems. At its most successful, simulation has become a ‘third way’ for scientists and engineers, complementing analytical and experimental methods. In engineering in particular, computational fluid dynamics simulation and finite element analysis are now an integral part of any design effort.

Similarly, we believe that physics-based simulation, in the form of molecular dynamics simulation, has great potential to become one of the basic tools in biochemical, and biophysical R&D, and establish itself as a robust tool in the drug discovery pipeline. Recent work, for example, has demonstrated the ability of MD simulation to produce quantitative estimates of small molecule binding kinetics (PNAS) and of conformational selection in selection in proteins (Nat. Comm., and blog).

Why perform molecular dynamics simulations on the cloud?

Currently, the amount of MD simulation required to undertake these types of studies is often beyond the reach of anyone without access to dedicated high-performance computing resources. To help overcome this critical limiting factor and bring MD simulation to a wider audience, we are pleased to introduce our new product AceCloud.

AceCloud is designed to free you from the constraints of your workstation and – though the use of cloud computing technology – allow you to run hundreds of simulations with the same ease as running one without the need of any additional setup.

Performing cloud molecular dynamics simulations with AceCloud

Accessing AceCloud is a simple matter of using three new commands built into the ACEMD molecular dynamics software package: for running simulations, retrieving results, and monitoring progress. No additional knowledge is required – our software takes care of all of the interaction with the Cloud. Here’s a video of AceCloud in action:

No changes are required to your existing ACEMD simulations, and all features are supported, including extensions and plugins such as PLUMED Metadynamics. As a bonus, users who are already familiar with Gromacs may run their existing simulation inputs on AceCloud, without the need to make any conversions.

The compute resources behind AceCloud are GPU-based and allow simulation rates over 100ns/day for the DHFR benchmark, making them around 40% as fast as the very latest GTX980s in our Metrocubo workstation, but still offering a compelling, cost-effective, level of performance.

AceCloud Costs

AceCloud uses Amazon Web Services (AWS) technology to dynamically provision compute hardware as and when you require it. The only charges for AceCloud are for the time used, from less than 0.40 US$ per hour. There are no minimum or on-going fees. There is no setup required and you can start using it at your convenience in just a few steps. Billing is hassle free and it is done through your own existing Amazon account.

You can calculate representative costs using our AceCloud Cost Estimator in the AceCloud page (this estimate already includes data transfer costs).

Start using AceCloud Today!

AceCloud is available right now. Visit our website for details on getting started.

mattAceCloud – Simplified, Limitless Molecular Dynamics Simulations on the Cloud