{'fraction_non_alphanumeric': 0.028052805280528052, 'fraction_numerical': 0.00935093509350935, 'mean_word_length': 5.404929577464789, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 1, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
Development of Molecular Dynamics Simulation System for Large-Scale Supra-Biomolecules, PABIOS (PArallel BIOmolecular Simulator)

The Earth Simulator has the highest power ever achieved to perform molecular dynamics simulation of large-scale supramolecular systems. Now, we are developing a molecular dynamics simulation system, called PABIOS, which is designed to run a system composed of more than a million particles efficiently on parallel computers. To perform large-scale simulations rapidly and accurately, state-of-the-art algorithms, such as Particle-Particle Particle-Mesh (PPPM) which can compute the long-range Coulomb interaction accurately and efficiently, are implemented. PABIOS uses a domain decomposition method which can achieve high parallelization. To optimize the load balance among the processors, the dynamic load-balancing algorithm was developed, and the assignment of subcells in the decomposition method for parallel computations to processors was automatically adjusted during the molecular dynamics simulation. Moreover, to make up for the insufficient parallel efficiency ratio of the PM calculation of PPPM, we have limited the number of processors which deal with the PM calculation and assigned the rest of the processors to other calculations. In order to improve the performance of PABIOS on the Earth Simulator, the algorithm to calculate short-range interactions (PP interactions) was intensively vectorized. A benchmark test was carried out using the system of a RuvA-Holliday junction DNA complex which consisted of 166,177 atoms. At present, PABIOS has achieved a parallelization efficiency ratio of 55.0%, and a vectorization ratio of 97.5% even when 15 nodes (120 processors) are used. As a result, the speed of calculation is about twice as fast as that of last fiscal year.