M.DynaMix – a scalable portable parallel MD simulation package for arbitrary molecular mixtures Original Research Article

A general purpose, scalable parallel molecular dynamics package for simulations of arbitrary mixtures of flexible or rigid molecules is presented. It allows use of most types of conventional molecular-mechanical force fields and contains a variety of auxiliary terms for inter- and intramolecular interactions, including an harmonic bond-stretchings. It can handle both isotropic or ordered systems. Besides an NVE MD ensemble, the simulations can also be carried out in either NVT or NPT ensembles, by employing the Nosé–Hoover thermostats and barostats, respectively. If required, the NPT ensemble can be generated by maintaining anisotropic pressures. The simulation cell can be either cubic, rectangular, hexagonal or a truncated octahedron, with corresponding periodic boundary conditions and minimum images. In all cases, the optimized Ewald method can be used to treat the Coulombic interactions. Double time-step or constrained dynamics schemes are included. An external electric field can be applied across the simulation cell. The whole program is highly modular and is written in standard Fortran 77. It can be compiled to run efficiently both on parallel and sequential computers. The inherent complexity of the studied system does not affect the scalability of the program. The scaling is good with the size of the system and with the number of processors. The portability of the program is good, it runs regularly on several common single- and multiprocessor platforms, both scalar and vector architectures included.