sDMD: An open source program for discontinuous molecular dynamics simulation of protein folding and aggregation

Discontinuous molecular dynamics (DMD) is an extremely fast alternative to the conventional molecular dynamics that uses continuous force fields. It simulates the force field applied to particles by discontinuous steplike functions of inter-particle distance. Thus, particles move at constant velocities until their distance is equal to the point at which there is a discontinuity, at which time the simulator calculates the interactions by solving simultaneously the equations governing conservation of momentum and energy. In this way, longer-time simulations can be carried out. Here, we introduce sDMD, an open source simulation package based on DMD technique coupled with a high-resolution all-atom molecular model, and describe the model of proteins, the algorithms for approximating the interactions, and the general design principles used in the simulator. We also demonstrate the implementation of the package, as well as two illustrative examples.