DFG priority programme 1648

People involved

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Helmut Grubmüller

Director

Phone:+49 551 201-2300Fax:+49 551 201-2302

Helmut's homepage

Berk Hess

Department of Theoretical Physics, School of Engineering Sciences, Royal Institute of Technology, SE-100 44 Stockholm

Holger Dachsel

Jülich Supercomputing Centre, Institute for Advanced Simulation, Mathematics Division, Leo-Brandt Str., 52425 Jülich

http://www.fz-juelich.de/ias/jsc/EN/

Ivo Kabadshow

Jülich Supercomputing Centre, Institute for Advanced Simulation, Mathematics Division, Leo-Brandt Str., 52425 Jülich

http://www.fz-juelich.de/ias/jsc/EN/

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Thomas Ullmann

Postdoc

Phone:+49 551 201-2303Fax:+49 551 201-2302

Thomas' homepage

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Carsten Kutzner

Software developer

Phone:+49 551 201-2313Fax:+49 551 201-2302

Carsten's homepage

Department of Theoretical and Computational Biophysics

Unified long-range electrostatics and dynamic protonation for realistic biomolecular simulations on the Exascale

In this DFG supported project we target a flexible, portable and scalable solver for potentials and forces, which is a prerequisite for exascale applications in particle-based simulations with long-range interactions in general. As a particularly challenging example that will prove and demonstrate the capability of our concepts, we use the popular molecular dynamics (MD) simulation software GROMACS. MD simulation has become a crucial tool to the scientific community, especially as it probes time- and length scales difficult or impossible to probe experimentally. Moreover, it is a prototypic example of a general class of complex multiparticle systems with long-range interactions.

MD simulations elucidate detailed, time-resolved behaviour of biology’s nanomachines. From a computational point of view, they are extremely challenging for two main reasons. First, to properly describe the functional motions of biomolecules, the long-range effects of the electrostatic interactions must be explicitly accounted for. Therefore, techniques like the particle-mesh Ewald method were adopted, which, however, severely limits the scaling to a large number of cores due to global communication requirements. The second challenge is to realistically describe the time-dependent location of (partial) charges, as e.g. the protonation states of the molecules depend on their time-dependent electrostatic environment. Here we address both tighly interlinked challenges by the development, implementation, and optimization of a unified algorithm for long-range interactions that will account for realistic, dynamic protonation states and at the same time overcome current scaling limitations.

 
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