Molecular dynamics simulations of molecules in uniform ow (Biophysical Journal)

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.