Artem Zhmurov

TL;DR: In this article, the authors present the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade, which involves a general cluster-based approach to pair lists and non-bonded pair interactions that utilizes both GPU and central processing unit (CPU) single instruction.

TL;DR: It is found that mechanical unraveling of fibrin(ogen) is determined by the combined molecular transitions that couple stepwise unfolding of the γ chain nodules and reversible extension-contraction of the α-helical coiled-coil connectors.

TL;DR: This work presents the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade, and enables excellent performance from single GPU simulations through strong scaling across multiple GPUs and efficient multi-node parallelization.

TL;DR: The soft α-to-β phase transition in coiled coil connectors of the human fibrin(ogen) molecule might be a universal mechanism underlying mechanical properties of filamentous α-helical proteins.

TL;DR: It is found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10‐fold increase in vf, implying that, to resolve accurately the free energy landscape and to relate the results of single‐molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads.