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Short{range molecular dynamics simulations of molecular systems are commonly parallelized by replicated{data methods, where each processor stores a copy of all atom positions. This enables computation of bonded 2{, 3{, and 4{body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the inter{processor communication scales ...

In this study we investigated the interaction behavior between thirteen different small peptides and a hydrophobic surface using three progressively more complex methods of representing solvation effects: a united-atom implicit solvation method [CHARMM 19 force field (C19) with Analytical Continuum Electrostatics (ACE)], an all-atom implicit solvation method (C22 with GBMV), and an all-atom exp...

The purpose of subgroup 2 is to computationally demonstrate and visualize the structural changes of proteins using COSMOS90 which can efficiently simulate proteins in water with all degrees of freedom and long-range Coulomb interactions. The purpose of our first stage (in 2003) was the acceleration of COSMOS90 on the Earth Simulator by vectorization and parallelization. The performance speed wa...