CompIF: Efficient computation of intermolecular forces for biomolecular simulations

Molecular simulations enable the structure, dynamics, and interactions of biomolecules to be explored in detail. Trajectories (or movies) of the evolution of molecular systems with time are generated by solving the equations of motion repeatedly at small time intervals. Molecules move due to the forces on them, and therefore the accurate computation of the forces is critical.  However, the computation of forces is generally the most computationally demanding part of a molecular simulation. Therefore, efficient algorithms and approximations are required to simulate biomolecular systems.

In this HITS Lab project, we will improve the computation of intermolecular forces in Brownian dynamics simulations of protein diffusion performed with the SDA software package developed in the MCM group. For this purpose, fast, hardware-aware solvers to compute forces will be implemented in the HiFlow3 finite element software package developed in the DMQ group. Interfaces between the two software packages will be constructed and machine learning methods employed to generate simulation trajectories efficiently. The results will expand the application range of Brownian dynamics simulations for studying proteins in dilute and macromolecularly crowded environments.

Contributors:

Rebecca Wade (MCM)
Vincent Heuveline (DMQ)

Member:

Riccardo Beccaria (MCM)