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DL_POLY_3 is a general-purpose massively parallel molecular dynamics simulation package embedding a highly efficient set of methods and algorithms such as: Domain Decomposition (DD), Linked Cells (LC), Daresbury Advanced Fourier Transform (DAFT), Trotter derived Velocity Verlet (VV) integration and RATTLE. Written to support academic research, it has a wide range of applications and can run on a wide range of computers; from single processor workstations to multi-processor computers. The code development has placed particular emphasis on the efficient utilization of multi-processor power by optimised memory workload and distribution, which makes it possible to simulate systems of the order of tens of millions of particles and beyond. In this paper we discuss the new DL_POLY_3 design, and report on the performance, capability and scalability. We also discuss new features implemented to simulate highly non-equilibrium processes of radiation damage and analyse the structural damage during such processes. have introduced the Domain Decomposition (DD) 10 version, DL_POLY_3, to permit simulation of systems of the order of tens of millions of atoms and beyond. As we shall see in the Performance and discussion section, DL_POLY_3's inherent parallelism allows close to perfect parallelisation up to impressively high processor counts.

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We present a new efficient Monte Carlo method for the molecular-based computer simulation of chemical systems undergoing any combination of reaction and phase equilibria. The method requires only a knowledge of the species intermolecular potentials and their ideal-gas properties, in addition to specification of the system stoichiometry and thermodynamic constraints. It avoids the calculation of chemical potentials and fugacities, as is similarly the case for the Gibbs ensemble method for phase equilibrium simulations. The method’s simplicity allows it to be easily used for situations involving any number of simultaneous chemical reactions, reactions that do not conserve the total number of molecules, and reactions occurring within or between phases. The basic theory of the method is presented, its relationship to other approaches is discussed, and applications to several simple example systems are illustrated.

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We present a new and computationally efficient methodology using osmotic ensemble Monte Carlo (OEMC) simulation to calculate chemical potential-concentration curves and the solubility of aqueous electrolytes. The method avoids calculations for the solid phase, incorporating readily available data from thermochemical tables that are based on well-defined reference states. It performs simulations of the aqueous solution at a fixed number of water molecules, pressure, temperature, and specified overall electrolyte chemical potential. Insertion/deletion of ions to/from the system is implemented using fractional ions, which are coupled to the system via a coupling parameter λ that varies between 0 (no interaction between the fractional ions and the other particles in the system) and 1 (full interaction between the fractional ions and the other particles of the system). Transitions between λ-states are accepted with a probability following from the osmotic ensemble partition function. Biasing weights associated with the λ-states are used in order to efficiently realize transitions between them; these are determined by means of the Wang-Landau method. We also propose a novel scaling procedure for λ, which can be used for both nonpolarizable and polarizable models of aqueous electrolyte systems. The approach is readily extended to involve other solvents, multiple electrolytes, and species complexation reactions. The method is illustrated for NaCl, using SPC/E water and several force field models for NaCl from the literature, and the results are compared with experiment at ambient conditions. Good agreement is obtained for the chemical potential-concentration curve and the solubility prediction is reasonable. Future improvements to the predictions will require improved force field models.

Thirteen of the most common aqueous NaCl solution force fields based on the SPC/E water solvent are examined with respect to their prediction at ambient conditions of the concentration dependence of the total electrolyte chemical potential and the solution density. We also calculate the salt solubility and the chemical potential and density of the NaCl crystalline solid. We obtain the solution chemical potential in a computationally efficient manner using our recently developed Osmotic Ensemble Monte Carlo method [F. Moučka, M. Lísal, and W. R. Smith, J. Phys. Chem. B 116, 5468 (2012)]. We find that the results of the force fields considered are scattered over a wide range of values, and none is capable of producing quantitatively accurate results over the entire concentration range, with only two of them deemed to be acceptable. Our results indicate that several force fields exhibit precipitation at concentrations below the experimental solubility limit, thus limiting their usefulness. This has important implications, both in general and for their use in biomolecular simulations carried out in the presence of counter-ions. We conclude that either different parameter fitting techniques taking high-concentration properties into account must be used when determining force field model parameters, or that the class of models considered here is intrinsically incapable of the task and more sophisticated mathematical forms must be used.