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SDSC Helps Enhance CHARMM Community Code to Study Key Reaction

PI: John Brady (Cornell), Mark Nimlos, Mike Himmel (both NREL/DOE), and Xianghong Qian (Colorado School of Mines), Linghao Zhong (Penn State), Charles L. Brooks III (TSRI)
SAC Staff: Ross Walker (SDSC), Mike Crowley (TSRI), Giri Chukkapalli (formerly SDSC)


The National Renewable Energy Laboratory (NREL) is striving to develop efficient large-scale conversion of biomass into ethanol to provide a clean-burning and renewable fuel source. This can have benefits from reducing dependence on fossil fuels and imported oil to protecting the climate. A key bottleneck in making this process economically viable is the slow breakdown of cellulose by the enzyme cellulase, and scientists want to understand this process at the molecular level so that they can target further research to speed up this important reaction.

Charmm
Figure 1. To improve the conversion of biomass into ethanol, NREL researchers simulated the action of the enzyme cellulase on cellulose using the CHARMM code. Left to right: the binding domain (blue), the glycosylated linker (green), and the catalyst domain (orange and yellow). NREL, Cornell, TSRI, Colorado School of Mines.

To explore the intricate molecular dynamics of this process, the researchers have used the CHARMM (Chemistry at HARvard Molecular Mechanics) code, a versatile community code for simulating biological reactions. But the size of new simulations needed is so large (more than one million atoms) and the simulation times so long (more than 5,000 time steps for the 10 or more nanosecond simulation) that they exceed the current capabilities of CHARMM.

Now researchers at the San Diego Supercomputer Center (SDSC) are working with colleagues at NREL, Cornell, the Scripps Research Institute, and the Colorado School of Mines to enhance CHARMM so that the simulations can scale up to millions of atoms and run on hundreds of processors on today's largest supercomputers, including SDSC's DataStar and the TeraGrid. This will make it feasible to simulate this key reaction.

The research is enabling the largest simulations ever of an important scientific problem that will yield economic and environmental benefits, and in addition, the improvements to the CHARMM code that will continue to be available for the scientific community to use on a wide range of other problems.


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