Christian Holm

ESPResSo—an extensible simulation package for research on soft matter systems

Abstract We describe a new program package that is designed to perform numerical Molecular Dynamics (MD) and Monte Carlo (MC) simulations for a broad class of soft matter systems in a parallel computing environment. Our main concept in developing ESPResSo was to provide a user friendly and fast simulation tool which serves at the same time as a research platform capable of rapidly incorporating the latest algorithmic developments in the field of soft matter sciences. A particular strength of ESPResSo is its efficient treatment of long range interactions for various geometries using sophisticated algorithms like P 3 M, MMM2D, MMM1D and ELC. It is already equipped with a broad variety of interaction potentials, thermostats, and ensemble integrators; it offers the usage of constraints, masses and rotational degrees of freedom; it allows to move between different ensembles on-the-fly. An efficient MPI parallelization allows the usage of multi-processor architectures. Strict usage of ANSI-C for the core functions and a Tcl -script driven user interface makes ESPResSo platform independent. This also ensures easily modifiable interfaces to communicate with other MD/MC Packages, real-time visualization and other graphic programs. We tried to maintain a clear program structure to keep ESPResSo extensible for future enhancements and additions. ESPResSo is implemented as an open source project with the goal to stimulate researchers to contribute to the package.

How to Mesh up Ewald Sums. I. A Theoretical and Numerical Comparison of Various Particle Mesh Routines

Standard Ewald sums, which calculate, e.g., the electrostatic energy or the force in periodically closed systems of charged particles, can be efficiently speeded up by the use of the fast Fourier transformation (FFT). In this article we investigate three algorithms for the FFT-accelerated Ewald sum, which have attracted widespread attention, namely, the so-called particle–particle–particle mesh (P3M), particle mesh Ewald (PME), and smooth PME method. We present a unified view of the underlying techniques and the various ingredients which comprise those routines. Additionally, we offer detailed accuracy measurements, which shed some light on the influence of several tuning parameters and also show that the existing methods — although similar in spirit — exhibit remarkable differences in accuracy. We propose a set of combinations of the individual components, mostly relying on the P3M approach, that we regard to be the most flexible. The issue of estimating the errors connected with particle mesh routines i...

How to mesh up Ewald sums. II. An accurate error estimate for the particle–particle–particle-mesh algorithm

We construct an accurate estimate for the root mean square force error of the particle–particle–particle mesh (P3M) algorithm by extending a single particle pair error measure which has been given by Hockney and Eastwood. We also derive an easy to use analytic approximation to the error formula. This allows a straightforward and precise determination of the optimal splitting parameter (as a function of system specifications and P3M parameters) and hence knowledge of the force accuracy prior to the actual simulation. The high quality of the estimate is demonstrated in several examples.

Force Fields for Studying the Structure and Dynamics of Ionic Liquids: A Critical Review of Recent Developments

Classical molecular dynamics simulations are a valuable tool to study the mechanisms that dominate the properties of ionic liquids (ILs) on the atomistic and molecular level. However, the basis for any molecular dynamics simulation is an accurate force field describing the effective interactions between all atoms in the IL. Normally this is done by empirical potentials which can be partially derived from quantum mechanical calculations on simple subunits or have been fitted to experimental data. Unfortunately, the number of accurate classical non-polarizable models for ILs that allow a reasonable description of both dynamical and statical properties is still low. However, the strongly increasing computational power allows one to apply computationally more expensive methods, and even polarizable-force-field-based models on time and length scales long enough to ensure a proper sampling of the phase space. This review attempts to summarize recent achievements and methods in the development of classical force fields for ionic liquids. As this class of salts covers a large number of compounds, we focus our review on imidazolium-based ionic liquids, but show that the main conclusions are valid for non-imidazolium salts, too. Insight obtained from recent electronic density functional results into the parametrization of partial charges and on the influence of polarization effects in bulk ILs is highlighted. An overview is given of different available force fields, ranging from the atomistic to the coarse-grained level, covering implicit as well as explicit modeling of polarization. We show that the recently popular usage of the ion charge as fit parameter can looked upon as treating polarization effects in a mean-field matter.

Electrostatic Effects in Soft Matter and Biophysics

Preface. List of Participants. Structure and dynamic properties of membrane lipid and protein M. Caffrey. Cell model and Poisson-Boltzmann theory: A brief introduction M. Deserno, C. Holm. DNA Condensation and Complexation W.M. Gelbart. Interactions in Colloidal Suspensions D.G. Grier, S.H. Behrens. Computer Simulations of charged systems C. Holm, K. Kremer. Scaling description of charged polymers J.-F. Joanny. When Ion-Ion Correlations Are Important in Charged Colloidal Systems B. Jonsson, H. Wennerstrom. Direct Surface Force Measurement Techniques P. Kekicheff. Counterions in polyelectrolytes A.R. Khokhlov, et al. Distribution function theory of electrolytes and electrical double layers R. Kjellander. Field-Theoretic Approaches to Classical Charged Systems A.G. Moreira, R.R. Netz. Interactions and conformational fluctuations in macromolecular arrays R. Podgornik. Structure and phasebehavior of cationic-lipid DNA complexes J.O. Radler. Small angle scattering methods applied to polyelectrolyte solutions M. Rawiso. Lateral correlation of multivalent counterions is the universal mechanism of charge inversion T.T. Nguyen, et al. Highly Charged Polyelectrolytes: experimental aspects C.E. Williams. Index.

Advanced Computer Simulation Approaches for Soft Matter Sciences III

Dunweg et al.: Lattice Boltzmann Simulations for Soft Matter Systems.- Kroll, Gomper et al.: Direct Particle Collosion Methods for Polymers and Membranes.- Eveaers, Grest, Kremer: Entangled Melts and Networks.- Dellago et al.: Transition Path Sampling an other Advances Sampling Techniques.-

Molecular dynamics study on the equilibrium magnetization properties and structure of ferrofluids

We investigate in detail the initial susceptibility, magnetization curves, and microstructure of ferrofluids in various concentration and particle dipole moment ranges by means of molecular dynamics simulations. We use the Ewald summation for the long-range dipolar interactions, take explicitly into account the translational and rotational degrees of freedom, coupled to a Langevin thermostat. When the dipolar interaction energy is comparable with the thermal energy, the simulation results on the magnetization properties agree with the theoretical predictions very well. For stronger dipolar couplings, however, we find systematic deviations from the theoretical curves. We analyze in detail the observed microstructure of the fluids under different conditions. The formation of clusters is found to enhance the magnetization at weak fields and thus leads to a larger initial susceptibility. The influence of the particle aggregation is isolated by studying ferro-solids, which consist of magnetic dipoles frozen in at random locations but which are free to rotate. Due to the artificial suppression of clusters in ferrosolids the observed susceptibility is considerably lowered when compared to ferrofluids.

Osmotic coefficients of atomistic NaCl (aq) force fields

Solvated ions are becoming increasingly important for (bio)molecular simulations. But there are not much suitable data to validate the intermediate-range solution structure that ion-water force fields produce. We compare six selected combinations of four biomolecular Na-Cl force fields and four popular water models by means of effective ion-ion potentials. First we derive an effective potential at high dilution from simulations of two ions in explicit water. At higher ionic concentration multibody effects will become important. We propose to capture those by employing a concentration dependent dielectric permittivity. With the so obtained effective potentials we then perform implicit solvent simulations. We demonstrate that our effective potentials accurately reproduce ion-ion coordination numbers and the local structure. They allow us furthermore to calculate osmotic coefficients that can be directly compared with experimental data. We show that the osmotic coefficient is a sensitive and accurate measure for the effective ion-ion interactions and the intermediate-range structure of the solution. It is therefore a suitable and useful quantity for validating and parametrizing atomistic ion-water force fields.

Modeling the separation of macromolecules: a review of current computer simulation methods.

Theory and numerical simulations play a major role in the development of improved and novel separation methods. In some cases, computer simulations predict counterintuitive effects that must be taken into account in order to properly optimize a device. In other cases, simulations allow the scientist to focus on a subset of important system parameters. Occasionally, simulations even generate entirely new separation ideas! In this article, we review the main simulation methods that are currently being used to model separation techniques of interest to the readers of Electrophoresis. In the first part of the article, we provide a brief description of the numerical models themselves, starting with molecular methods and then moving towards more efficient coarse‐grained approaches. In the second part, we briefly examine nine separation problems and some of the methods used to model them. We conclude with a short discussion of some notoriously hard‐to‐model separation problems and a description of some of the available simulation software packages.

Effect of Anions on Static Orientational Correlations, Hydrogen Bonds, and Dynamics in Ionic Liquids: A Simulational Study

Three different ionic liquids are investigated via atomistic molecular dynamics simulations using the force field of Lopes and PAdua (J. Phys. Chem. B 2006, 110, 19586). In particular, the 1-ethyl-3-methylimidazolium cation EMIM+ is studied in the presence of three different anions, namely, chloride Cl-, tetrafluoroborate BF(4)(-), and bis((trifluoromethyl)sulfonyly)imide TF2N-. In the focus of the present study are the static distributions of anions and cations around a cation as a function of anion size. It is found that the preferred positions of the anions change from being close to the imidazolium hydrogens to being above and below the imidazolium rings. Lifetimes of hydrogen bonds are calculated and found to be of the same order of magnitude as those of pure liquid water and of some small primary alcohols. Three kinds of short-range cation-cation orderings are studied, among which the offset stacking dominates in all of the investigated ionic liquids. The offset stacking becomes weaker from [EMIM][Cl] to [EMIM][BF4] to [EMIM][TF2N]. Further investigation of the dynamical behavior reveals that cations in [EMIM][TF2N] have a slower tumbling motion compared with those in [EMIM][Cl] and [EMIM][BF4] and that pure diffusive behavior can be observed after 1.5 ns for all three systems at temperatures 90 K above the corresponding melting temperatures.