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.

We present a GPU accelerated CUDA-C implementation of the Barnes Hut (BH) tree code for calculating the gravitational potential on octree adaptive meshes. The tree code algorithm is implemented within the FLASH4 adaptive mesh refinement (AMR) code framework and therefore fully MPI parallel. We describe the algorithm and present test results that demonstrate its accuracy and performance in comparison to the algorithms available in the current FLASH4 version. We use a MacLaurin spheroid to test the accuracy of our new implementation and use spherical, collapsing cloud cores with effective AMR to carry out performance tests also in comparison with previous gravity solvers. Depending on the setup and the GPU/CPU ratio, we find a speedup for the gravity unit of at least a factor of 3 and up to 60 in comparison to the gravity solvers implemented in the FLASH4 code. We find an overall speedup factor for full simulations of at least factor 1.6 up to a factor of 10.

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