The SOP-GPU package, where SOP stands for the Self Orginized Polymer Model fully implemented on a GPU, is a scientific software package designed to perform Langevin Dynamics Simulations of the mechanical or thermal unfolding, and mechanical pulling/indentation of large biomolecular systems in the experimental subsecond (millisecond-to-second) timescale. The SOP-GPU package utilizes the \(C_\alpha\) and \(C_\alpha\)-\(C_\beta\) based coarse-grained description of proteins combined with computational power of modern Graphics Processing Units (GPUs).
- Self-Organized Polymer model
- Generation of pseudo-random numbers on graphics processors
- Using SOP-GPU program
- Input parameters file
Examples of SOP-GPU configurational files can be found here.