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Primeur weekly 2014-02-24

Special

H2020: the long road to an integrated open and accessible European e-Infrastructure ...

PRACE, HPC applications and technological development: three ingredients for a top European strategy ...

Yannick Legré is the new director of EGI.eu ...

The Cloud

Red Hat Enteprise Linux OpenStack Platform leveraged by Alcatel-Lucent, CloudBand as part of its Network Functions Virtualization (NFV) Platform ...

AT&T and IBM join forces to deliver new innovations for the Internet of Things ...

Mellanox introduces CloudX Platform to enable companies to build the most efficient public, private and hybrid Clouds ...

EuroFlash

Powerful supercomputer to offer a glimpse of the early universe ...

From a distance: New technique for repair work ...

ECRIN-ERIC to host inauguration ceremony ...

Karlsruhe Institute of Technology to develop ultra-small and ultra–fast electro-optic modulator ...

SURFsara to host Data & Computing Infrastructure Event on 12-13 March 2014 ...

USFlash

SDSC team develops multi-scale simulation software for chemistry research ...

SDSC/UC San Diego researchers hone in on Alzheimer's disease ...

Intel advances next phase of Big Data intelligence: real time analytics ...

Supercomputer dramatically accelerates rapid genome analysis ...

Using computers to speed up drug discovery ...

Better cache management could improve chip performance and cut energy use ...

A step closer to a photonic future ...

HP delivers record-breaking performance and dramatic efficiencies with HP ProLiant servers ...

Researchers propose a better way to make sense of 'Big Data' ...

Mega-bucks from Russia seed development of 'Big Data' tools ...

A new laser for a faster Internet ...

C-DAC to organize Accelerating Biology 2014: Computing Life ...

NetApp introduces unified scale-out storage systems and virtualization software for the unbound Cloud era ...

Supermicro shipping 96 DIMM 4U 4-Way SuperServer featuring new Intel Xeon processor E7-8800/4800 v2 ...

SDSC team develops multi-scale simulation software for chemistry research


19 Feb 2014 San Diego - Researchers at the San Diego Supercomputer Center (SDSC) at the University of California, San Diego, have developed software that greatly expands the types of multi-scale QM/MM - mixed quantum and molecular mechanical - simulations of complex chemical systems that scientists can use to design new drugs, better chemicals, or improved enzymes for biofuels production.

A paper outlining the research, titled "An Extensible Interface for QM/MM Molecular Dynamics Simulations with AMBER" and conducted by members of the Walker Molecular Dynamics Lab (WMD) at SDSC, was featured on the cover of the January 15th issue of theJournal of Computational Chemistry.

Multi-scale QM/MM computational methods are crucial to advancing the understanding and solution to problems in the chemical sciences, ranging from drug design to renewable energies. This has been recognized with the award of the 2013 Nobel Prize in chemistry for the development of multi-scale models of complex chemical systems.

In QM/MM simulations, an accurate but computationally complex and thus time-consuming quantum mechanical model is used to identify important features of the electronic structure of a chemically relevant region. This is required, for example, to describe photo-physical processes or chemical reactions in the active site of enzymes. Effects of the surrounding environment are then included with a computationally less complex classical MM model.

"QM/MM simulations are computationally very demanding compared to purely classical MM simulations", stated Ross C. Walker, an SDSC research professor and adjunct associate professor in UC San Diego's Department of Chemistry and Biochemistry. "Access to SDSC's Trestles and Gordon supercomputers and their fast turnaround times were essential to our work. We ran a large amount of jobs to test and validate our implementation at various stages, as well as a large-scale simulation to demonstrate a practical application."

"Our software enables QM/MM simulations with a variety of advanced quantum mechanical models, and by integrating it with the popular AMBER molecular simulation package, which is used by hundreds of academic and industrial research labs, we can reach a very large user base", stated lead author Andreas W. Goetz, a research scientist with SDSC and expert in multi-scale modelling. "We're looking forward to many exciting applications that will help scientists in computational chemistry and biophysics understand and predict the behavior of molecular systems at a fundamental level."

Authors of the new study include SDSC's Andreas W. Goetz and Ross C. Walker as well as Matthew A. Clark, who developed part of the software during his internship with Ross C. Walker and Andreas W. Goetz, as part of SDSC's Research Experience for High School Students (REHS) programme and later as an undergraduate research intern in the WMD lab.

The paper is available at Wiley Online Library .

Source: San Diego Supercomputer Center - SDSC

Back to Table of contents

Primeur weekly 2014-02-24

Special

H2020: the long road to an integrated open and accessible European e-Infrastructure ...

PRACE, HPC applications and technological development: three ingredients for a top European strategy ...

Yannick Legré is the new director of EGI.eu ...

The Cloud

Red Hat Enteprise Linux OpenStack Platform leveraged by Alcatel-Lucent, CloudBand as part of its Network Functions Virtualization (NFV) Platform ...

AT&T and IBM join forces to deliver new innovations for the Internet of Things ...

Mellanox introduces CloudX Platform to enable companies to build the most efficient public, private and hybrid Clouds ...

EuroFlash

Powerful supercomputer to offer a glimpse of the early universe ...

From a distance: New technique for repair work ...

ECRIN-ERIC to host inauguration ceremony ...

Karlsruhe Institute of Technology to develop ultra-small and ultra–fast electro-optic modulator ...

SURFsara to host Data & Computing Infrastructure Event on 12-13 March 2014 ...

USFlash

SDSC team develops multi-scale simulation software for chemistry research ...

SDSC/UC San Diego researchers hone in on Alzheimer's disease ...

Intel advances next phase of Big Data intelligence: real time analytics ...

Supercomputer dramatically accelerates rapid genome analysis ...

Using computers to speed up drug discovery ...

Better cache management could improve chip performance and cut energy use ...

A step closer to a photonic future ...

HP delivers record-breaking performance and dramatic efficiencies with HP ProLiant servers ...

Researchers propose a better way to make sense of 'Big Data' ...

Mega-bucks from Russia seed development of 'Big Data' tools ...

A new laser for a faster Internet ...

C-DAC to organize Accelerating Biology 2014: Computing Life ...

NetApp introduces unified scale-out storage systems and virtualization software for the unbound Cloud era ...

Supermicro shipping 96 DIMM 4U 4-Way SuperServer featuring new Intel Xeon processor E7-8800/4800 v2 ...