Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


SDSC Team Develops Multi-scale Simulation Software for Chemistry Research

SDSC’s Trestles and Gordon supercomputers used in development and validation

Researchers at the San Diego Supercomputer Center 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 the Journal 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,” said 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”, said lead author Andreas W. Goetz, a research scientist with SDSC and expert in multi-scale modeling. “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 Goetz and Walker as well as Matthew A. Clark, who developed part of the software during his internship with Walker and Goetz, as part of SDSC’s Research Experience for High School Students (REHS) program and later as an undergraduate research intern in the WMD lab.

Media Contact

Jan Zverina, 858-534-5111,
Secondary media contact:
Warren R. Froelich, 858 822-3622,

Jan Zverina | EurekAlert!
Further information:

More articles from Life Sciences:

nachricht Molecular doorstop could be key to new tuberculosis drugs
20.03.2018 | Rockefeller University

nachricht Modified biomaterials self-assemble on temperature cues
20.03.2018 | Duke University

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Mars' oceans formed early, possibly aided by massive volcanic eruptions

Oceans formed before Tharsis and evolved together, shaping climate history of Mars

A new scenario seeking to explain how Mars' putative oceans came and went over the last 4 billion years implies that the oceans formed several hundred million...

Im Focus: Tiny implants for cells are functional in vivo

For the first time, an interdisciplinary team from the University of Basel has succeeded in integrating artificial organelles into the cells of live zebrafish embryos. This innovative approach using artificial organelles as cellular implants offers new potential in treating a range of diseases, as the authors report in an article published in Nature Communications.

In the cells of higher organisms, organelles such as the nucleus or mitochondria perform a range of complex functions necessary for life. In the networks of...

Im Focus: Locomotion control with photopigments

Researchers from Göttingen University discover additional function of opsins

Animal photoreceptors capture light with photopigments. Researchers from the University of Göttingen have now discovered that these photopigments fulfill an...

Im Focus: Surveying the Arctic: Tracking down carbon particles

Researchers embark on aerial campaign over Northeast Greenland

On 15 March, the AWI research aeroplane Polar 5 will depart for Greenland. Concentrating on the furthest northeast region of the island, an international team...

Im Focus: Unique Insights into the Antarctic Ice Shelf System

Data collected on ocean-ice interactions in the little-researched regions of the far south

The world’s second-largest ice shelf was the destination for a Polarstern expedition that ended in Punta Arenas, Chile on 14th March 2018. Oceanographers from...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

Virtual reality conference comes to Reutlingen

19.03.2018 | Event News

Ultrafast Wireless and Chip Design at the DATE Conference in Dresden

16.03.2018 | Event News

International Tinnitus Conference of the Tinnitus Research Initiative in Regensburg

13.03.2018 | Event News

Latest News

Physicists made crystal lattice from polaritons

20.03.2018 | Physics and Astronomy

Mars' oceans formed early, possibly aided by massive volcanic eruptions

20.03.2018 | Physics and Astronomy

Thawing permafrost produces more methane than expected

20.03.2018 | Earth Sciences

Science & Research
Overview of more VideoLinks >>>