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Gunther Lukat

Adresse:

Gojenbergsweg 112

21029 Hamburg

Büro: Beamtenwohnhaus, R. 004

Telefon: ++49 40 42838 8407

Gunther Lukat Scientific Page of the Observatory

Research interest:

  • Numerical Simulations
  • Scientifc Programming
  • GPU/MIC Programming

Projects:

A GPU accelerated Barnes Hut gravity tree code for FLASH4:

This project is aimed to accelerate the existing gravity module in the astrophysical simulation code FLASH4. We implement our own version of a massive parallel Barnes & Hut tree code. We use the well known LET (local essential tree) approach an moved the tree building and the tree walks to the GPU device. Although the code is still under development, we reached a speedup of the gravity unit of over factor 30. You can download the GPU accelerated Gravity solver here: GPU-BH Tree

APL@VORO:A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories.

APL@Voro is a new program developed to aid in the analysis of GROMACS trajectories of lipid bilayer simulations. It can read a GROMACS trajectory file, a PDB coordinate file, and a GROMACS index file to create a two-dimensional geometric representation of a bilayer. Voronoi diagrams and Delaunay triangulations--generated for different selection models of lipids--support the analysis of the bilayer. The values calculated on the geometric structures can be visualized in a user-friendly interactive environment and, then, plotted and exported to different file types. APL@Voro supports complex bilayers with a mix of various lipids and proteins. For the calculation of the projected area per lipid, a modification of the well-known Voronoi approach is presented as well as the presentation of a new approach for including atoms into an existing triangulation. The application of the developed software is discussed for three example systems simulated with GROMACS. The program is written in C++, is open source, and is available free of charge. For more information about APL@VORO see: APL@VORO

Publications:

Lukat, G.; Krüger, J.; Sommer, B. APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories. J. Chem. Inf. Model. 2013, 53, 2908â~@~S 2925

Sommer, B.; Gamroth, C.; Heissmann, A. J.; Lukat, G.; Rotzoll, R.; Rubert, S.; Schäfer, A.; Krüger, J. The GMX-Plugin for the CELLmicrocosmos MembraneEditor. J. Cheminformatics 4.S-1 (2012): P49.

Sommer, B.; T Dingersen, T.; C Gamroth, C.; Heissmann, A.J.; Lukat, G.; Rotzoll, R.; Rubert, S.; Schäfer, A.; Krüger, J. Coarse-grained and all-atom MD simulations with Gromacs based on CELLmicrocosmos 2.2 model membranes. J. Cheminformatics 3.S-1 (2011): P43.