The SOP-GPU package, where SOP-GPU stands for the Self Orginized Polymer Model fully implemented on a Graphis Processing Unit (GPUs), is a scientific software package designed to perform Langevin Dynamics Simulations of the mechanical pulling/indentation of large biomolecular systems on the experimental subsecond (millisecond-to-second) timescale. The SOP-GPU package utilizes the Cα-atom based coarse-grained description of proteins combined with Langevin Dynamics in overdamped limit and computational power of modern GPUs.
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gpu, biomechanics, biophysics, coarse-graining, nanoindentation, protein-model, graphic-processing-unit, atomic-force-microscopy, large-biomolecule, molecular-dynamic-simulations, langevin-dynamics, self-organized-polymer-model