Showing papers in "Molecular Simulation in 1994"

A Comparison of Particle-Particle, Particle-Mesh and Ewald Methods for Calculating Electrostatic Interactions in Periodic Molecular Systems

Abstract: We compare the Particle-Particle Particle-Mesh (PPPM) and Ewald methods for calculating electrostatic interactions in periodic molecular systems. A brief comparison of the theories shows that the methods are very similar differing mainly in the technique which is used to perform the “k-space” or mesh calculation. Because the PPPM utilizes the highly efficient numerical Fast Fourier Transform (FFT) method it requires significantly less computational effort than the Ewald method and scales almost linearly with system size.

Optimisation of the Ewald Sum for Large Systems

Abstract: Techniques are described for optimising the Ewald sum in the simulation of systems containing large numbers of charged particles. Expressions are given for the best choice of parameters to maximise performance for a specified accuracy. The algorithm for the real-space sum uses a “small-cell” version of the link-cell method. Various other computational details are discussed. In the simulation of real systems there is considerable scope for speeding the calculation by redcing cutoffs, without loss of accuracy.

On The Berendsen Thermostat

Abstract: The behaviour of the total momentum of a system immersed in the Berendsen thermostat is analyzed. It has been found that under certain conditions the kinetic energy of the system can be transformed from internal degrees of freedom to the external ones, and conversely. A concrete example of such a transformation is presented. The results of molecular dynamics simulations of the Fe4S4(SH)4 complex coupled to different external heat baths are discussed.

An Interatomic Potential Model for H2O: Applications to Water and Ice Polymorphs

Abstract: A new interatomic potential model for H2O which consists of 2-body central (O-H, O-O and H-H) and 3-body teams and does not contain artificial constraints on the motions of oxygen and hydrogen atoms is proposed. The interatomic potential function parameters were determined empirically so as to reproduce the fundamental and essential features of water and ice Ih using molecular dynamics (MD) methods. We carried out the MD simulations of water, and find the Ice Ih, Ice II and Ice IX using this potential model, in structures and physical properties are in agreement with the experimental results except for the compressibilities of both water and ice Ih. We expect that, by refining this model, we can apply this model to problems involving the reaction of water molecules with other components.

Scaled Particle Theory and the Efficient Calculation of the Chemical Potential of Hard Spheres in the NVT Ensemble

Abstract: We propose and test a new method for calculating the chemical potential of a hard-sphere fluid using Monte Carlo calculations in the NVT ensemble, which we call the SP-MC method. The method employs ideas from scaled particle theory (SPT), including a recent new SPT result of Smith and Labik for hard-sphere mixtures. The method is based on the calculation of the chemical potential at infinite dilution of a series of hard spheres of smaller diameter than that of the system of interest. Using this easily obtained data in conjunction with theoretical considerations, the chemical potential of the hard-sphere system may be accurately obtained. The SP-MC method is more precise than any other currently available method, and it can be used up to extremely high densities, including into the metastable region.

A Grand Canonical Monte-Carlo Study of Lennard-Jones Mixtures in Slit Pores; 2: Mixtures of Two Centre Ethane with Methane

Abstract: Mixtures of ethane and methane in a slit micropore were simulated using the Grand Canonical Monte Carlo technique Ethane was modelled as two Lennard-Jones sites while methane was modelled as a single Lennard-Jones site The elongated shape of ethane was found to strongly influence the calculated adsorption selectivity, and important qualitative differences were noted relative to an earlier GCMC study (Cracknell et al, Molec Phys Vol 80, pp 885–897, 1993) in which ethane was modelled as a spherical Lennard-Jones particle The influence of ethane bond length on methane-ethane selectivity was studied further by conducting simulations with the ethane C[sbnd]C distance 28% and then 70% longer than its actual length; the hindrance of rotation by confinement in the micropore was found to cause a significant decrease in selectivity The Ideal Adsorbed Solution Theory was found to predict the selectivities with a reasonable degree of accuracy given simulated single component data as input

A noniterative matrix-method for constraint molecular-dynamics simulations

Abstract: A non-iterative version of the matrix method which can be easily vectorised and parallelized is presented. The original matrix method, which is conceptually identical to the familiar SHAKE algorithm, is shown to be non-iterative when incorporated with the Verlet and leap-frog integration schemes with the same constraint error order as the (local) error order of the accompanying integration schemes. The method is checked by test simulations with n-butane and the liquid crystal moleculae 5CB (4-n-pentyl-4′-cyanobiphenyl) in which its effectiveness is demonstrated.

A CFF 91-based Continuum Solvation Model: Solvation Free Energies of Small Organic Molecules and Conformations of the Alanine Dipeptide in Solution

Abstract: For molecular mechanics simulations of solvated molecules, it is important to use a consistent approach for calculating both the force field energy and the solvation free energy. A continuum solvation model based upon the atomic charges provided with the CFF91 force field is derived. The electrostatic component of the solvation free energy is described by the Poisson-Bolzmann equation while the nonpolar comonent of the solvation energy is assumed to be proportional to the solvent accessible surface area of the solute. Solute atomic radii used to describe the interface between the solute and solvent are fitted to reproduce the energies of small organic molecules. Data for 140 compounds are presented and compared to experiment and to the results from the well-characterized quantum mechanical solvation model AM1-SM2. In particular, accurate results are obtained for amino acid neutral analogues (mean unsigned error of 0.3 kcal/mol). The conformational energetics of the solvated alanine dipeptide is d...

Extension and Simple Proof of Lekner's Summation Formula for Coulomb Forces

Abstract: In [3] J Lekner derived an elegant and very useful summation formula for Coulomb forces In his derivation he used some powerful identities such as the Poisson-Jacobi identity, the application of which was not at all straightforward In this note it is shown that Lekner's result and an extension to more general potentials can be obtained in a rather simple and straightforward way

Phase Diagrams of Diatomic Molecules Using the Gibbs Ensemble Monte Carlo Method

Abstract: The Gibbs simulation method is used to explore the phase diagrams of a range of diatomic Lennard-Jones (DLJ) molecules. The dependence of the critical packing fractions on the bond-length of the molecules is examined. Reasonable agreement is found with both experimental and theoretical results. Particular attention is paid to the phase diagram of chlorine and the phase diagram is predicted for a more accurate anisotropic site-site potential. Good agreement is found with the experimental results for both the potential models. We conclude that for chlorine, the liquid-vapour phase envelope is not sensitive to the details of the potential model and therefore cannot be used to improve the model of the intermolecular forces.

On Multiple Time-step Algorithms and the Ewald Sum

Abstract: We show how standard multiple time-step algorithms devised for systems with short-range potentials can be used successfully in simulations of periodic systems with long-range (Coulombic) potentials. Three strategies for incorporating the Ewald sum into a multiple time-step algorithm are considered. These are (i) evaluation of reciprocal space terms every time-step (ii) evaluating reciprocal space terms once every n time-steps and placing these terms in with the slowly varying forces and energies (iii) a modified form of the second strategy in which primary shell (close) electrostatic interactions are evaluated directly and the more distant interactions handled by the Ewald sum (once every n time-steps). Only the first and third approaches give satisfactory thermodynamic results. The third strategy is much more efficient than the first. With the third strategy substantial savings in cpu time are acheived in both the real space and, most importantly, the reciprocal space terms of the Ewald sum. Thi...

A Parallel Algorithm for Nonequilibrium Molecular Dynamics Simulation of Shear Flow on Distributed Memory Machines

Abstract: An algorithm is described which allows Nonequilibrium Molecular Dynamics (NEMD) simulations of a fluid undergoing planar Couette flow (shear flow) to be carried out on a distributed memory parallel processor using a (spatial) domain decomposition technique. Unlike previous algorithms, this algorithm uses a co-moving, or Lagrangian, simulation box. Also, the shape of the simulation box changes throughout the course of the simulation. The algorithm, which can be used for two or three dimensional systems, has been tested on a Fujitsu AP1000 Parallel computer with 128 processors.

Monte Carlo Implementation on the Connection Machine 2; Water in Graphite Pores

Abstract: The implementation of Monte Carlo (Canonical and Grand Canonical Ensembles) codes on the Single Instruction Multi Data parallel supercomputer Connection Machine 2 are discussed and demonstrated. The program was developed for the simulation of water behavior in slit graphite pores in CM FORTRAN. A one dimensional data layout is the most suitable for MC realization on the CM-2. The code performance is compared with the performance of sequential and parallel codes on other computers. Preliminary results of the simulations are reported.

The Genetic Algorithm and the Conformational Search of Polypeptides and Proteins

Abstract: The genetic algorithm is a technique of function optimization derived from the principles of evolutionary theory We have adapted it to perform conformational search on polypeptides and proteins The algorithm was first tested on several small polypeptides and the 46 amino acid protein crambin under the AMBER potential energy function The probable global minimum conformations of the polypeptides were located 90% of the time and a non-native conformation of crambin was located that was 150kcal/mol lower in potential energy than the minimized crystal structure conformation Next, we used a knowledge-based potential function to predict the structures of melittin, pancreatic polypeptide, and crambin A 231 A ΔRMS conformation of melittin and a 533 A ΔRMS conformation of pancreatic polypeptide were located by genetic algorithm-based conformational search under the knowledge-based potential function Although the ΔRMS of pancreatic polypeptide was somewhat high, most of the secondary structure was c

Membrane Crossing by a Polar Molecule: A Molecular Dynamics Simulation

Abstract: This paper is concerned with the permeability of a glycerolipid bilayer to a polar molecule. We have simulated by molecular dynamics the interaction between a molecule of dimethyl sulfoxide (DMSO) and a membrane of glycerol monoleate in solution. We find that the structure of the membrane is affected only locally by the crossing of the polar molecule. The DMSO molecule opens a hole at the surface of the bilayer which allows a water molecule to penetrate inside. This water is then expelled as the DMSO penetrates more deeply inside. Finally we find that the energetics of crossing is affected by structural transformations occuring on a timescale of 20 ps and over.

A New Potential Model for Carbon Dioxide from AB Initio Calculations

Abstract: Ab initio quantum chemical calculations have been carried out for carbon dioxide dimer and the results have been used to establish potential functions usable in molecular simulations. Since the intermolecular interaction in carbon dioxide is fairly weak, careful treatment is required: this study uses 6–31G* basis set and takes electron correlations by the 2nd order Moller-Plesset theory into account. The potential energy surface is elucidated using the four representative relative configurations of the dimer. A new potential function model has been proposed on the basis of these ab initio data. In the super-critical region, this model is used to calculate the PVT relation of carbon dioxide fluid by the Monte Carlo simulations and confirmed to reproduce reasonably well the experimental isotherms.

Grand Canonical Ensemble Monte Carlo Simulations of Donnan Potentials, Nonelectroneutrality, Activity Coefficients and Excess Energy in Spherical Charged or Uncharged Pores with Restricted Primitive Model Electrolytes

Abstract: A great number of Grand Canonical Ensemble simulations have been performed for restricted primitive model electrolytes in spherical hard-wall pores with the same dielectric permittivity in the pores and in the wall. The pores have a continuously distributed surface charge from 0 to 10 elementary charges and radii from 1 to 35 ionic diameters. When a pore is in equilibrium with an outside bulk solution, it acquires in the average a certain deviation from electroneutrality (spontaneous electrification). For any given pore surface charge this electrification is a given function of the radius of the accessible part of the pore scaled by the Debye length without regard to the Debye length without regard to the Bjerrum parameter or the bulk concentration of the electrolyte and without regard to the pore size relative to the ion diameter. If an additional uniform electric potential is applied in the pore, the electrification changes. At a certain potential the pore is electroneutral. This potential is a...

Simulation of lamellar phase transitions in block copolymers and surfactants

Abstract: Simulations of the lamellar phase transitions of symmetric amphiphilic chains are carried out on a cubic lattice, with the amphiphilic chain length N varied from 6 to 48 lattice sites, corresponding to lengths ranging from surfactants to short block copolymers. We find that the effective interaction energy parameter χN (which incorporates the effect of added solvant) at which the transition from the lamellar ordered state to the disordered state occurs is roughly equal to 18-21. While this result is consistent with an extrapolation of the Fredrickson-Helfand weak-segragation theory to N values in the range of the simulations, the amplitude of the sinusoidal compositional wave in the ordered state near the transition is large for all N studied, in disagreement with the weak segregation theories. Thus, for values of N up to 48, the transition occurs in a “moderate,” rather than weak-segregation regime. Near the disordering transition, fluctuating “bridge” or “hole” defects in the lamellae spontaneo...

Brownian Dynamics Simulation of DNA Gel Electrophoresis

Abstract: Brownian dynamics computer simulation technique was applied to investigate DNA dynamics in gel electrophoresis. Under a constant electric field of moderate strength, large DNA chains take stretched and contracted conformations alternatively during the migration. The conformation change is quasi-periodic under certain conditions, and its frequency is closely related to the experimentally-found suitable frequency of pulse field gel electrophoresis.

A Comparision of Methods for Computing Transition Rates from Molecular Dynamics Simulation

Abstract: Correlation function and direct counting methods for the evaluation of the isomerization rates in equilibrium molecular dynamics (MD) simulations are studied for a system of 64 independent particles, each undergoing transitions between two stable states according to a Poisson process. Three different numerical implementations of the number correlation function and two different counting formulas based on different ordering of averages over trajectory and particles are tested. All methods yield correct results for sufficiently long simulations. However, for simulations where a given particle undergoes a small (< 5-10) number of transitions, accurate rates are obtained only when the correlation function is normalized after averaging over particles; this correlation function is shown to be equivalent to the relaxation function of Brown and Clarke (J. Chem. Phys. 92, 3062, 1990). Similarily, accurate rates are obtained with a counting formula where the average first passage time is first calculated o...

On the Stability of Clathrate Hydrates Encaging Polar Guest Molecules: Contrast in the Hydrogen Bonds of Methylamine and Methanol Hydrates

Abstract: The stability of clathrate hydrates encaging highly polar guests has been investigated in order to explain the experimental observation that some amines form clathrate hydrates but alcohols act as inhibitor to hydrate formation. We choose methylamine and methanol as guest species and examine the stable structure, at which the total potential energy has a minimum value. At the local minima of those two hydrates, the potential energies of water-water and guest-water, and their hydrogen bonded networks are compared. It is found that methanol does not retain the host lattice structure, while the host-network structure is kept in the presence of methylamine. It is shown that the difference in the magnitude of the partial charge on the hydrogen atom between the hydroxyl and amino groups plays a much more significant role on the stability of both clathrate hydrates than the difference in molecular geometry. This is supported from the result of a methylamine-like model that has the same partial charges o...

Molecular-Dynamics Simulation of the Surface Diffusion of n-Alkanes on Pt(111)

Abstract: In the present study, the equilibrium adsorption and the dynamics of surface diffusion in a model of ethane and n-butane on a Pt(111) surface were simulated with molecular dynamics At low temperatures, we found that both admolecules adsorb in a specific binding site Through analysis of the trajectories, several features of the dynamics were resolved At low temperature, we observed that diffusion occurs through a nearest-neighbor hopping mechanism involving both lateral rotation and axial translation At high temperatures, the admolecule makes multiple-site hops and nonlocalized long flights The temperature dependence of the diffusion coefficients was analyzed and was found to exhibit good Arrhenius behavior The apparent diffusion coefficients follow trends seen in related experimental studies In the case of ethane, a comparison between the diffusion barrier measured in the molecular-dynamics simulations and the theoretical barrier predicted by transition-state theory indicates that the simu

Calculation of the generalized susceptibility for a highly supercooled fluid through molecular-dynamics simulation

Abstract: A new method of computation of generalized susceptibility and dynamical structure factor through molecular dynamics (MD) simulation is proposed. This gives rise to a reliable and accurate result more than that calculated from a conventional method with a direct Fourier transformation. Computational results are presented for the imaginary part of the generalized susceptibility, X″ (ω), for a binary soft-sphere fluid with a super-long-time molecular dynamics (MD) simulation. Both α- and β-peaks in X″ (ω) in a supercooled fluid is shown for the first time through the present MD computation. The MD result obtained is in a good agreement with that obtained by the trapping diffusion model, which we have previously proposed for the glass transition.

Molecular Dynamics Simulations of Langmuir-Blodgett Monolayers with Explicit Head-group Interactions

Abstract: Energy minimisation and molecular dynamics calculations have been performed for models of Langmuir-Blodgett films containing stearic acid molecules. The model includes a specific representation of the atoms and dipole moment of the carboxylic acid head-group. Simulations have been performed at head-group areas per molecule of 20.6 A2 and 21.2 A2 at room temperature. This all-atom model predicts significant conformational disorder at the torsional angle connecting the head-group to the hydrocarbon chain. The strong charge/image-charge interaction doubles the tilt of the layer over that found for the united-atom Lennard-Jones head-group. The dipoles of the head-group are alined parallel to the surface forming a two sub-lattice structure in the plane of the surface.

The Stability of Clathrate Hydrates: Temperature Dependence of Dissociation Pressure in Xe and Ar Hydrate

Abstract: The thermodynamic stability of clathrate hydrates I and II encaging xenon or argon has been investigated by examining the temperature dependence of the dissociation pressure. The evaluation of the stability is made based on the generalized van der Waals and Platteeuw theory developed by Tanaka and Kiyohara [J. Chem. Phys. 98, 4098 (1993)]. In the new treatment, the free energy of formation of hydrates in equilibrium with ice is calculated by taking the coupling of the host lattice vibrations with guests into consideration. The predicted dissociation pressures of Xe and Ar hydrates agree well with experiments in higher temperature range. A poor agreement between experiment and calculation for Ar clathrate hydrate at low temperature is improved by the use of a quantum mechanical partition function for a harmonic oscillator in evaluating the free energy difference between ice and empty hydrate.

Evaporation and Condensation at a Liquid Surface of Methanol

Abstract: Evaporation and condensation processes at a liquid surface of methanol were investigated at room temperature with a microcanonical molecular dynamics computer simulation technique. The condensation coefficient (the number ratio of condensed molecules to incident ones) was estimated by comparing two types of autocorrelation functions, and found to be less than unity, which is in qualitative agreement with experiments. A variety of complex dynamic phenomena were observed at the surface.

A Computational Study of Oxygen Ordering in YBa2Cu3Oz and its Relation to Superconductivity

Abstract: An ab initio model to study oxygen ordering in the high temperature superconductor YBa2Cu3Oz is presented. The phase diagram computed with this model contains several ordered structures and is in excellent agreement with the known experimental information. At high temperature, an orthorhombic structure transforms by a second order reaction into a tetragonal structure. At low temperature, a branching algorithm generates an infinity of ordered structures all consisting of long O–Cu–O chains. By looking at the kinetic evolution of quenched samples in a Monte Carlo simulation it was possible to clarify how annealing of the material can influence its superconducting transition temperature.

Molecular Dynamics Simulations With First Order Coupling to a Bath of Constant Chemical Potential

Abstract: In molecular dynamics simulations the temperature or pressure can be controlled by applying a weak first-order coupling to a bath of constant temperature or pressure. This weak coupling technique to control system properties using a first-order relaxation equation is analyzed from a statistical mechanics point of view. It is shown, how the weak coupling scheme can be generalized and applied to a bath of contstant chemical potential. The presented method, to which in the following will be referred to as chemical potential weak coupling, is applied and tested on a Lennard-Jones fluid. The thermodynamic quantities known from the literature are accuratly reproduced. The temperature and chemical potential weak coupling methods aim to sample the canonical and grand canonical ensembles respectively. By analyzing the fluctuations in energy and number of particles, the tight relation between the ensembles and the distributions obtained from the weak coupling simulations is demonstrated. The influence of t...

An application of classical molecular dynamics simulation and ab initio density-functional calculation in surface physics

Abstract: Classical molecular dynamics simulation and ab initio mixed basis Car-Parrinello methods are discussed and applied to the investigation of the results of a recently performed STM-based experiment involving the adsorption of C60 molecules on the dimerized Si surface. We show that these methods are capable of providing the theoretical basis for this experiment and test the validity of the associated conjectures. A mixed-basis all-electron formalism for the Car-Parrinello method is proposed to obtain the detailed understanding of the electronic states and dynamics of surface structure. A band structure calculation using this formalism is performed for the c(4 × 3) structure of C60 adsorbed on Si (100) surface and is compared with the experimental results.

Rotational Motion of Linear Molecules in Three Dimensions. A Path-Integral Monte Carlo Approach

Abstract: A path-integral Monte Carlo (PIMC) simulation method for the rotational motion of linear molecules in three dimensions is presented. The technique is applied to an H2 impurity in a static crystal-field. The resulting orientational distributions from quantum and classical simulations are obtained and discussed. The algorithm suffers from the “sign problem” of quantum simulations. However, as can be seen by comparing the low temperature simulation result to the variational solution of the Schrodinger equation, the PIMC method captures the quantum fluctuations.