Developing a hybrid continuum-particle method for simulating large-scale heterogeneous biomolecular systems
Sean Seyler, Ohio Supercomputer Center
Usage DetailsSteven Gordon, Sean Seyler
A parallel hybrid numerical algorithm will be implemented that combines the accuracy of all-atom molecular dynamics (AAMD) in a restricted subdomain with the computational frugality of a continuum model external to the region of direct interest. Starting with an existing 3D Navier-Stokes (NS) MPI-based code and a production MD engine like NAMD, I propose to: (1) augment the NS code to model fluctuating hydrodynamics, (2) implement a parallel coupling scheme to handle flux-/state-based boundary conditions across the particle-continuum interface, and (3) perform a sequence of tests on reference systems—from a Lennard-Jones fluid up to a solvated polymer system—to examine whether the hybrid code agrees with conventional AAMD simulations.