Steffen Reiser

ms2: A molecular simulation tool for thermodynamic properties, new version release

Abstract A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation to achieve higher scalability. Furthermore, the formalism by Lustig [R. Lustig, Mol. Phys. 110 (2012) 3041] is implemented, allowing for a systematic sampling of Massieu potential derivatives in a single simulation run. Moreover, the Green–Kubo formalism is extended for the sampling of the electric conductivity and the residence time. To remove the restriction of the preceding version to electro-neutral molecules, Ewald summation is implemented to consider ionic long range interactions. Finally, the sampling of the radial distribution function is added. Program summary Program title: m s 2 Catalogue identifier: AEJF_v2_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEJF_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 50375 No. of bytes in distributed program, including test data, etc.: 345786 Distribution format: tar.gz Programming language: Fortran90. Computer: The simulation program m s 2 is usable on a wide variety of platforms, from single processor machines to modern supercomputers. Operating system: Unix/Linux. Has the code been vectorized or parallelized?: Yes: Message Passing Interface (MPI) protocol and OpenMP Scalability is up to 2000 cores. RAM: m s 2 runs on single cores with 512 MB RAM. The memory demand rises with increasing number of cores used per node and increasing number of molecules. Classification: 7.7, 7.9, 12. External routines: Message Passing Interface (MPI) Catalogue identifier of previous version: AEJF_v1_0 Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 2350 Does the new version supersede the previous version?: Yes. Nature of problem: Calculation of application oriented thermodynamic properties for fluids consisting of rigid molecules: vapor–liquid equilibria of pure fluids and multi-component mixtures, thermal and caloric data as well as transport properties. Solution method: Molecular dynamics, Monte Carlo, various classical ensembles, grand equilibrium method, Green–Kubo formalism, Lustig formalism Reasons for new version: The source code was extended to introduce new features. Summary of revisions: The new features of Version 2.0 include: Hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation; Ewald summation for long range interactions; sampling of Massieu potential derivatives; extended Green–Kubo formalism for the sampling of the electric conductivity and the residence time; radial distribution function. Restrictions: None. The system size is user-defined. Typical problems addressed by m s 2 can be solved by simulating systems containing typically 1000–4000 molecules. Unusual features: Auxiliary feature tools are available for creating input files, analyzing simulation results and visualizing molecular trajectories. Additional comments: Sample makefiles for multiple operation platforms are provided. Documentation is provided with the installation package and is available at http://www.ms-2.de . Running time: The running time of m s 2 depends on the specified problem, the system size and the number of processes used in the simulation. E.g. running four processes on a “Nehalem” processor, simulations calculating vapor–liquid equilibrium data take between two and 12 hours, calculating transport properties between six and 24 hours. Note that the examples given above stand for the total running time as there is no post-processing of any kind involved in property calculations.

Molecular dispersion energy parameters for alkali and halide ions in aqueous solution

Thermodynamic properties of aqueous solutions containing alkali and halide ions are determined by molecular simulation. The following ions are studied: Li(+), Na(+), K(+), Rb(+), Cs(+), F(-), Cl(-), Br(-), and I(-). The employed ion force fields consist of one Lennard-Jones (LJ) site and one concentric point charge with a magnitude of ±1 e. The SPC/E model is used for water. The LJ size parameter of the ion models is taken from Deublein et al. [J. Chem. Phys. 136, 084501 (2012)], while the LJ energy parameter is determined in the present study based on experimental self-diffusion coefficient data of the alkali cations and the halide anions in aqueous solutions as well as the position of the first maximum of the radial distribution function of water around the ions. On the basis of these force field parameters, the electric conductivity, the hydration dynamics of water molecules around the ions, and the enthalpy of hydration is predicted. Considering a wide range of salinity, this study is conducted at temperatures of 293.15 and 298.15 K and a pressure of 1 bar.

A Set of Molecular Models for Alkaline-Earth Cations in Aqueous Solution

New Lennard-Jones plus point charge models are developed for alkaline-earth cations. The cation parameters are adjusted to the reduced liquid solution density of aqueous alkaline-earth halide salt solutions at a temperature of 293.15 K and a pressure of 1 bar. This strategy is analogous to the one that was recently used for developing models for alkali and halide ions so that both model families are compatible. The force fields yield the reduced liquid solution density of aqueous alkaline-earth halide solutions in good agreement with experimental data over a wide range of salinity. Structural microscopic properties (i.e. radial distribution function and hydration number) are predicted in good agreement with experimental and quantum chemical data. The same holds for dynamic properties (i.e., hydration dynamics, self-diffusion coefficient and electric conductivity). Finally, the enthalpy of hydration of the salts in aqueous solution was favorably assessed.

Solvent activity in electrolyte solutions from molecular simulation of the osmotic pressure

A method for determining the activity of the solvent in electrolyte solutions by molecular dynamics simulations is presented. The electrolyte solution is simulated in contact with the pure solvent. Between the two phases, there is a virtual membrane, which is permeable only for the solvent. In the simulation, this is realized by an external field which acts only on the solutes and confines them to a part of the simulation volume. The osmotic pressure, i.e., the pressure difference between both phases, is obtained with high accuracy from the force on the membrane, so that reliable data on the solvent activity can be determined. The acronym of the new method is therefore OPAS (osmotic pressure for activity of solvents). The OPAS method is verified using tests of varying complexity. This includes a comparison of results from the OPAS method for aqueous NaCl solutions to results from the literature which were obtained with other molecular simulation methods. Favorable agreement is observed not only for the solvent activity but also for the activity coefficient of NaCl, which is obtained by application of the Gibbs-Duhem equation.

Molecular Modelling and Simulation of Electrolyte Solutions, Biomolecules, and Wetting of Component Surfaces

Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and employed for the simulation of electrolytes in aqueous solution. The enzymatically catalysed hydroxylation of oleic acid is investigated by molecular dynamics simulation taking the internal degrees of freedom of the macromolecules into account. Thereby, Ewald summation methods are used to compute the long range electrostatic interactions. In systems with a phase boundary, the dispersive interaction, which is modelled by the Lennard-Jones potential here, has a more significant long range contribution than in homogeneous systems. This effect is accounted for by implementing the Janecek cutoff correction scheme. On this basis, the HPC infrastructure at the Steinbuch Centre for Computing was accessed and efficiently used, yielding new insights on the molecular systems under consideration.

Atomistic Simulations of Electrolyte Solutions and Hydrogels with Explicit Solvent Models

Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions), and of systems containing large molecules such as hydrogels. These tasks become particularly demanding when explicit solvent models are used. Therefore, massively parallel supercomputers are needed for both tasks.