Press Releases

Performing molecular dynamics simulations using GPUs

Read the interview made to <a href=”https://es.linkedin.com/in/gdefabritiis”>Dr Gianni de Fabritiis</a>, group leader at the Computational Biophysics Laboratory of the Research Programme on Biomedical Informatics within the Barcelona Biomedical Research Park. He makes a nice overview of the things his group is doing and the tools he has developed, about volunteer distributed computing and its importance in research. He also highlights the potential importance of the use of GPUs in computer aided drug design and some of the challenges of the molecular dynamics simulation research field.

gianniPerforming molecular dynamics simulations using GPUs
read more

Penguin Computing Showcases Acellera’s ACEMD at SC2012

PENGUIN COMPUTING SHOWCASES ACELLERA’S ACEMD AT SC2012 LONDON, UK – 10 November 2012

Acellera today announced that Penguin Computing will showcase Acellera’s ACEMD on POD (Penguin Computing ON Demand) at Supercomputing 2012 in Salt Lake City, Utah, booth 3866. ACEMD is the world’s fastest and most efficient bio-molecular dynamics (MD) engine for GPU nodes and workstations. Specifically optimized to run on NVIDIA graphics cards, ACEMD enables on a single GPU performance equivalent to more than 100 CPUs while maintaining microsecond trajectories. In combination with POD, ACEMD aims to facilitate the transition of MD from a multi-node, single-trajectory science to high-throughput MD (HT-MD), a new paradigm in computational biophysics.

Matt Jacobs, Sr. Vice President of Corporate Development for Penguin Computing states, “As we approach the clock cycle limits on traditional CPU architectures, multicore and GPU technologies are moving to the forefront to reshape the way our customers conceptualize their research. Acellera’s ACEMD package demonstrates the true capabilities that this new level of parallelism offers and Penguin Computing is pleased to be able to showcase this package on our POD environment at this year’s Supercomputing conference.”

Molecular Dynamics simulation is a powerful technique for investigating biological systems with atomic resolution. Prior to the introduction of Acellera’s ACEMD, the cost of bio-MD simulations for R&D was prohibitive, requiring hundreds of CPU cores for a single run on dedicated HPC clusters. ACEMD transformed the bio-MD field by introducing highly optimized bio-MD simulation on comparatively low-cost GPUs, enabling supercomputing class simulations on a small GPU cluster. ACEMD enables new kinds of analyses, such as the complete reconstruction of protein–ligand interactions in terms of thermodynamics and kinetics, or MD based fragment-based drug discovery. Such studies open new avenues in pharmaceutical research, and illuminate ligand binding site and pose, as well as specific kinetic signatures that can be associated with the quality of small molecules during drug development.

“We are pleased to have this opportunity to work with such a reputable provider of world-class HPC solutions. Penguin’s POD technology combined with Acellera’s ACEMD provides an unbeatable platform for on-demand, highly-efficiency bio-MD simulation for all scientists, from those just beginning to explore its huge potential to established MD users” states Gianni De Fabritiis, Founder and Chief Science Officer at Acellera.

ACEMD is the engine behind GPUGRID, one of the largest distributed computing projects worldwide. ACEMD is stable, scalable, robust, and can handle thousands of highly demanding MD simulations daily. ACEMD simulations have helped researchers push our understanding of protein-ligand interactions, ion channel dynamics, membrane protein behavior, and mechanisms for drug resistance.

Penguin Computing and Acellera are looking to expand their partnership to include turn-key solutions which integrate Acellera and Penguin technology. This would mark Penguin Computing as the first U.S. Value Added Reseller and provider of L1 system support for Metrocubo, Acellera’s MD appliance.

To experience a demonstration of ACEMD at SC2012, visit Penguin Computing booth 1217 November 12-15th where ACEMD simulations will use POD, an HPC cloud that provides instant availability on-demand. Interested parties will be offered the opportunity during those same dates to challenge ACEMD with their own systems on POD. Contact David Soriano at info@acellera.com for more information.

About Penguin Computing
For well over a decade Penguin Computing has been dedicated to delivering complete, integrated High Performance Computing (HPC) solutions that are innovative, cost effective and easy to use. Penguin offers a complete end-to-end portfolio of products and solutions ranging from Linux servers and workstations to integrated, turn-key HPC clusters and cluster management software. For users that want to use supercomputing capabilities on-demand and pay as they go, Penguin offers ‘Penguin Computing on Demand’ (POD), a public HPC cloud that is available instantly and as needed. With its broad portfolio of solutions Penguin is the one-stop shop for HPC and enterprise customers and counts some of the world’s most demanding HPC users as its customers, including Caterpillar, Life Technologies, Dolby, Lockheed Martin, the U.S. Air Force, and the U.S. Navy.
To learn more, visit http://www.penguincomputing.com

About Acellera
Acellera is a UK based company focused on providing new technologies in the field of research and development. Since 2006, Acellera has innovated in the field of molecular dynamics simulation software for accelerator processors. Its current flagship product, ACEMD, delivers cluster-computer levels of performance for MD simulations on personal GPU workstations. Computational throughput is also optimized through the joined development of software and hardware. Recently, Acellera designed and patented a new enclosure for GPU optimized calculations for these purposes.
One mission of Acellera is to develop high-throughput molecular dynamics techniques that deliver solutions for estimating common physical chemistry properties as binding affinities, kinetics, poses and pathways with experimental accuracy. The development of new methods for molecular data analysis allows us to understand binding processes to a new level of insight. In this field, the Binding Assay solution by Acellera provides a level of details on the binding process that is unique worldwide.
Acellera is the owner and unique provider of the intellectual property behind all these technologies and the software, hardware infrastructure.
To learn more, visit http://www.acellera.com

Penguin Computing is a registered trademark of Penguin Computing, Inc. Penguin Computing on Demand is a pending trademark in the U.S. ACEMD is a trademark of Acellera. All other trademarks are property of their respective owners. Other product or company names mentioned may be trademarks or trade names of their respective companies.

alejandroPenguin Computing Showcases Acellera’s ACEMD at SC2012
read more