In summary, we have developed a phase-field simulation of molecular dynamics. Our developed method has successfully stabilized a molecular structure with bond, angle and dihedral interactions. Moreover, our developed method directly provided time-averaged dynamics of MD simulations. Our simulation will be a powerful strategy to clarify molecule properties in a longer time scale. Figure : (a) Mesh generation schemes for an atom density. In scheme 1, a mesh is set at the global coordinate system as shown in (a1). Scheme 2 refers to a local coordinate system as shown in (a2). A small mesh, whose centre corresponds with the centre of an atom density, is generated. r is a position vector to the centre of an atom density from the global coordinate system. λ ′ is a displacement vector in the local coordinate system. (b) Comparison of computation time after 300 steps between schemes 1 and 2. In scheme 1, we considered 16∆x × 16∆x × 16∆x grids mesh at the global coordinate system. In scheme 2, a local mesh with 8∆x × 8∆x × 8∆x grids was considered. ∆x = 0.3 Å in both schemes.