Multiscale and Distributed Computing Algorithms for Biomolecular Simulation and Efficient Free Energy Calculations (ERIKLINDAHLERC2007)

Project leader

Funding source

EU Seventh Framework Programme - ERC Starting Grant

Project Details

Start date: 01/09/2008
End date: 31/08/2013
Funding: 992413 EUR


The long-term goal of our research is to advance the state-of-the-art in molecular simulation algorithms by 4-5 orders of magnitude, particularly in the context of the GROMACS software we are developing. This is an immense challenge, but with huge potential rewards: it will be an amazing virtual microscope for basic chemistry, polymer and material science research; it could help us understand the molecular basis of diseases such as Creutzfeldt-Jacob, and it would enable rational design rather than random screening for future drugs. To realize this, we will focus on four topics:
• Algorithms for simulation on graphics and other streaming processors Graphics cards and the test Intel 80-core chip are not only the most powerful processors available, but this type of streaming architectures will power many supercomputers in 3-5 years, and it is thus critical that we design new “streamable” MD algorithms.
• Multiscale modeling We will develop virtual-site-based methods to bridge atomic and mesoscopic dynamics, QM/MM, and mixed explicit/implicit solvent models with water layers around macromolecules.
• Multi-level parallel & distributed simulation Distributed computing provides virtually infinite computer power, but has been limited to small systems. We will address this by combining SMP parallelization and Markov State Models that partition phase space into transition/local dynamics to enable distributed simulation of arbitrary systems.
• Efficient free energy calculations We will design algorithms for multi-conformational parallel sampling, implement Bennett Acceptance Ratios, correction terms for PME lattice sums, and combine standard force fields with polarization/multipoles, e.g. Amoeba. We have a strong track record of converting methodological advances into applications, and the results will have impact on a wide range of fields from biomolecules and polymer science through material simulations. Further, we will focus our own applications on extreme-scale simulations to understand voltage-gated ion channels as well as drug design and free energy calculations targeting ion channels and transporters.

External Partners

Last updated on 2017-13-09 at 09:22