High-Performance Computing in the Molecular Dynamics of Tubulin Cytoskeleton Polymers
DOI:
https://doi.org/10.14529/jsfi260102Keywords:
molecular dynamics, tubulin, microtubule, CPU, GPU, computing performanceAbstract
High-performance computing is one of the most essential tools fueling the advancement of computational biology. The article discusses the application of the full-atom molecular dynamics (MD) method to study the dynamic behavior of filaments formed by the protein tubulin, and presents the results of testing the calculation performance depending on the latest models of central processors and video accelerators. Our comparative performance analysis of GPU-based computing architectures for all-atom MD simulations of biomolecular systems not only provides guidance on choosing the best computing solution in terms of price-performance ratio, but also shows the maximum potential computational performance that modern CPUs and GPUs can provide. For example, MD of the biomolecular system containing a tubulin protofilament in an explicitly specified solvent consisting of more than 300 thousand atoms can be studied with performance of 232 ns/day at time step 2 fs when using single-node computer with the latest CPU and GPU generation architecture. Constantly evolving computing resources coupled with modern software enable us to solve increasingly complex problems in life sciences.
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