M.DynaMix - a scalable portable parallel MD simulation package for arbitrary molecular mixtures

A general purpose, scalable parallel molecular dynamics package for simulat ions 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 int eractions, including an harmonic bond-stretchings. It can handle both isotr opic or ordered systems. Besides an NVEMD ensemble, the simulations can als o be carried out in either NVT or NPT ensembles, by employing the Nose-Hoov er thermostats and barostats, respectively. If required, the NPT ensemble c an be generated by maintaining anisotropic pressures. The simulation cell c an 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 interaction s. Double time-step or constrained dynamics schemes are included. An extern al electric held can be applied across the simulation cell. The whole progr am is highly modular and is written in standard Fortran 77. It can be compi led to run efficiently both on parallel and sequential computers. The inher ent 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 numb er of processors. The portability of the program is good, it runs regularly on several common single- and multiprocessor platforms, both scaler and ve ctor architectures included. (C) 2000 Elsevier Science B.V. All rights rese rved.