Molecular Dynamics Simulations of Molecules in Uniform Flow

Abstract Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of ow on molecules we present uniform ow Molecular Dynamics (MD) simulations at atomic level. The pull module of the GROMACS package was extended to be able to force group atoms within a de_ned layer of the simulation box. Application of this external enforcement to explicit water molecules, together with the coupling to a thermostat, led to a uniform terminal velocity of the solvent water molecules. We monitored the density of the whole system to establish the conditions under which the simulated ow is well-behaved. A maximal velocity generated of 1:3 m/s can be generated if a pull slice of 8nm is used, and high velocities would require larger pull slices to still maintain a stable density. As expected the target velocity increases linearly with the total external force applied. Finally, we suggest an appropriate setup to stretch a protein by uniform ow, where protein extensions depend on the ow conditions. Our implementation provides an e_cient computational tool to investigate the e_ect of the ow at the molecular level.