Jean-Paul Ryckaert

Molecular dynamics of liquid n-butane near its boiling point

Liquid n-butane has been simulated near its boiling point by the method of molecular dynamics. The computed self-diffusion coefficient D is approximately equal to 6.0 × 10−5 cm2/s; the corresponding velocity autocorrelation function displays practically no cage effect, differing markedly from argon and other simple fluids in this respect.

Molecular dynamics simulation of rigid molecules

Abstract This paper is a review of the method of constraints. The method was devised to carry out Molecular Dynamics simulations of complex molecular systems with some internal degrees of freedom frozen, in terms of atomic Cartesian coordinates. The method has been subsequently generalized to treat all kinds of holonomic constraints and has been adapted to the more recent dynamical simulations in ensembles different from the microcanonical one. We start by deriving the statistical-mechanical formalism for these systems. We then proceed to derive the equations of motion. We conclude with a detailed discussion of the relevant MD algorithms. Some technical details on the FORTRAN code are presented in an appendix.

Molecular dynamics of rigid systems in cartesian coordinates: A general formulation

The dynamics of rigid polyatomic systems, either molecules or rigid portions of large molecules, is described by cartesian equations of motion for its atoms. In comparison with the original version of the method of constraints

Observation, prediction and simulation of phase transitions in complex fluids

Preface. A: Experiment. Phase Transition of Spherical Colloids W.C.K. Poon, P.N. Pusey. Liquid Crystal Phase Transitions in Dispersions of Rodlike Colloidal Particles H.N.W. Lekkerkerker, P. Buining, J. Buitenhuis, G.J. Vroege, A. Stroobants. Phase Transitions in Colloidal Suspensions of Virus Particles S. Fraden. B: Theory. Colloidal Suspensions: Density Functional Theory at Work J.-P. Hansen. Bilayer Phases M.E. Cates. Liquid Crystal Interfaces M.M. Telo Da Gama. Statistical Mechanics of Directed Polymers D.R. Nelson. C: Simulation. Introduction to Monte Carlo Simulation M.P. Allen. Numerical Techniques to Study Complex Liquids D. Frenkel. Molecular Dynamics Techniques for Complex Molecular Systems M. Sprik. Gibbs Ensemble Techniques A.Z. Panagiotopoulos. Phase Transitions in Polymeric Systems K. Binder. Simulations and Phase Behaviour of Liquid Crystals M.P. Allen. D: Seminars. Equilibrium Sedimentation Profiles of Screened Charged Colloids. A Test of the Hard-Sphere Equation of State V. Degiorgio, R. Piazza, T. Bellini. Dynamics of N-Nonadecane Chains in Urea Inclusion Compounds as Seen by Incoherent Quasielastic Neutron Scattering and Computer Simulations M. Souaille, J.C. Smith, A.-J. Dianoux, F. Guillaume. Theory of Phase Equilibria in Associating Systems: Chain and Ring Aggregates, Amphiphiles, and Liquid Crystals R.P. Sear, G. Jackson. Can a Solid be Turned into a Gas Without Passing through a First Order Phase Transition? R. Lovett. Index.

Molecular dynamics of liquid alkanes

The method of molecular dynamics is applied to the simulation of liquid systems of n-alkanes. The model used is a semi-rigid one with fixed C—C bonds and C—C—C angles. In addition to the static and dynamic properties usually deduced for monatomic fluids from such computer experiments, the configurational properties and the internal relaxation behaviour of the alkane chain are also studied. The results of two different simulations of n-butane and of one simulation of n-decane are analysed. The usefulness and the limitations of such computer experiments are discussed briefly.

Special geometrical constraints in the molecular dynamics of chain molecules

The molecular dynamics simulation of chain molecules with a full atomic description is considered in the particular case of a n-alkane molecule. In order (a) to keep the time step in the numerical integration of the equations of motions to a reasonable value (10-15-10-14s) and (b) to describe such flexible systems with a minimum number of degrees of freedom, it is useful to impose geometrical constraints in order to freeze the fastest intramolecular motions of the chain. Given the large number and the nature of the geometrical constraints involved in this model, the method of constraints used to solve the dynamics in terms of atomic cartesian coordinates needs to be generalized to arbitrary constraints and solved in an iterative way. Such a method is proposed and illustrated on a ring alkane chain, namely cyclo-tetradecane (C14H28).

Disorder in the pseudohexagonal rotator phase of n-alkanes: molecular-dynamics calculations for tricosane

Molecular-dynamics calculations for a flexible-chain model have been used to study two, solid, bilayer phases of the n-alkane tricosane (C23H48). In the crystalline, orthorhombic phase at 311 K, the chains remain all-trans and fully ordered, with a herringbone packing. By contrast, in the pseudohexagonal (R I) rotator phase at about 320 K, a dramatic increase in longitudinal chain motion is observed, each chain has four well-defined orientations, and a significant number of conformational defects develop, with the latter occurring predominantly at the chain ends. The results of the simulations are in excellent agreement with experiment.

Constant pressure-constant temperature molecular dynamics for rigid and partially rigid molecular systems

The method of molecular dynamics at fixed pressure and/or temperature is adapted to rigid or partly rigid molecular systems with geometrical constraints using the cartesian coordinate approach. Both isotropic and anisotropic volume fluctuations, allowing for shape variation, are considered. The simulation of a benzene crystal at zero pressure and various temperatures is given as an illustration.

Translational and rotational disorder in solid n‐alkanes: Constant temperature–constant pressure molecular dynamics calculations using infinitely long flexible chains

Molecular dynamics calculations are used to study the effect of temperature on the interchain packing in solid n‐alkanes. The model used consists of infinite chains initially arranged in a centered orthorhombic structure with the lateral packing found in the low temperature phase of n‐alkanes with an odd number of carbon atoms. An atom–atom interchain potential is employed and the chains have flexible backbones. The problem of equilibrating the inter‐ and intramolecular motions is overcome using the technique of massive stochastic collisions proposed by Andersen. The calculated isobaric lateral thermal expansion of the orthohombic a and b cell parameters is in excellent agreement with experimental data over a wide temperature range. For T> 250 K translational (jump) diffusion is observed along the chain axis (c direction) without any accompanying rigid body chain rotation. At higher temperatures, the diffusion becomes liquid‐ like and rotational diffusion sets in between four well defined sites. Possible ...

Introduction of Andersen’s demon in the molecular dynamics of systems with constraints

The method of constant pressure molecular dynamics (MD), developed by Andersen for monoatomic fluids is extended to the MD, in Cartesian coordinates, of molecular systems with constraints. Andersen’s proof is easily generalized after decoupling internal degrees of freedom from the center‐of‐mass. Only these last degrees are directly affected by Andersen’s transformation (demon). The Cartesian equations of motion of individual atoms are derived from a generalized Andersen’s Lagrangian. The equations are quite similar to those of the usual MD simulation at constant volume apart from an additional term coupling the molecular center‐of‐mass and the volume of the sample. The volume appears now as a dynamical variable evolving from the imbalance between imposed external pressure and instantaneous values of the molecular stress tensor. Some numerical aspects are discussed and the technique is briefly illustrated for the case of rigid diatomic molecules.