As the size and complexity of structurally resolved biomolecules continues to increase, researchers require ever more powerful visualization and analysis tools to gain understanding of their function and dynamics. The latest release of VMD, the leading molecular dynamics visualization tool, has unleashed the computational power of graphics processing units (GPUs) and multi-core CPUs enabling researchers to interactively study large biomolecular complexes on desktop computers as a matter of daily routine. VMD 1.8.7 includes many new and improved graphics algorithms enabling fast rendering of high resolution photorealistic molecular scenes. New graphical representations and coloring features enable visualization of carbohydrates, nanodevice structures, and results of quantum chemistry simulations. Fast GPU electrostatics algorithms reduce or eliminate the need for batch mode calculations, e.g., for computing electrostatics of large systems, accelerating them by a factor of 22-44. The latest improvements to the MultiSeq plugin enable processing of up to 100,000 sequences on a desktop computer. New and updated structure building tools ease construction of large all-atom and coarse-grained molecular models.

Bacteria contain the simplest photosynthetic machineries found in nature. Higher organisms like algae and plants practice photosynthesis in a more elaborate but principally similar manner as bacteria. But even for its simplicity, the bacterial photosynthetic unit is not without its unsolved mysteries. Take, for example, the crucial photosynthetic core complex, which performs light absorption and the initial processing of the light energy. In certain bacterial species, the core complex contains two copies of an additional small protein (made of about 80 amino acids) called PufX, whose role in photosynthesis is still a puzzle, and its location within the core complex is yet to be pinpointed. Numerous imaging studies have been published, yielding two opinions on what the role of PufX is and where exactly it resides. One opinion assigns the protein the role of gate keeper, the other the role of coordinator. Recently, a computational investigation was carried out that much supports the second role. Since PufX comes as a pair, two copies of PufX were placed side-by-side in a biological membrane and they were seen to adhere to each other strongly, but assume with their cylindrical (helical) shape an angle of 38 degrees. This geometry is perfectly suited for PufX to join the two parts of the symmetrical core complex together in the middle and to impose on the parts the tilt that was actually observed in the imaging studies. The needed simulations were done with NAMD. More details can be found on our photosynthetic core complex website.