Explicit-solute implicit-solvent molecular simulation with binary level-set, adaptive-mobility, and GPU

Coarse-grained modeling and efficient computer simulations are critical to the study of complex molecular processes with many degrees freedom multiple spatiotemporal scales. Variational implicit-solvent model (VISM) for biomolecular solvation is such a framework, its initial success has been demonstrated consistently. In VISM, an effective free-energy functional solute-solvent interfaces minimized, surface energy key component free energy. this work, we extend VISM include solute mechanical interactions, develop fast algorithms GPU implementation extended variational explicit-solute (VESIS) determine underlying equilibrium conformations. We employ binary level-set method minimizing construct adaptive–mobility gradient descent atomic optimization. also implement our methods on integrated GPU. Numerical tests applications several systems verify accuracy, stability, efficiency algorithms. It found that new improve simulation significantly over CPU implementation. Our computational techniques may enable us simulate very large as protein-protein interactions membrane dynamics which explicit-solvent all-atom can be expensive.