Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

A many-body polarizable force field has been developed and validated for ionic liquids (ILs) containing 1-methyl-3-alkylimidazolium, 1-alkyl-2-methyl-3-alkylimidazolium, N-methyl-N-alkylpyrrolidinium, N-alkylpyridinium, N-alkyl-N-alkylpiperidinium, N-alkyl-N-alkylmorpholinium, tetraalkylammonium, tetraalkylphosphonium, N-methyl-N-oligoetherpyrrolidinium cations and BF4−, CF3BF3−, CH3BF3−, CF3SO3−, PF6−, dicyanamide, tricyanomethanide, tetracyanoborate, bis(trifluoromethane sulfonyl)imide (Ntf2− or TFSI−), bis(fluorosulfonyl)imide (FSI−) and nitrate anions. Classical molecular dynamics (MD) simulations have been performed on 30 ionic liquids at 298, 333, and 393 K. The IL density, heat of vaporization, ion self-diffusion coefficient, conductivity, and viscosity were found in a good agreement with available experimental data. Ability of the developed force field to predict ionic crystal cell parameters has been tested on four ionic crystals containing Ntf2− anions. The influence of polarization on the struc...

Polarizable Force Field Development and Molecular Dynamics Simulations of Ionic Liquids

A review of the theoretical and computational modeling of bimolecular reactions is given. The review is divided into several sections which are as follows: gas-phase thermal reactions; gas-phase state-selected reactions and product state distributions; and condensed-phase bimolecular reactions. The section on gas-phase thermal reactions covers the enthalpies and free energies of reaction, kinetics, saddle points and potential energy surfaces, rate theory for simple barrier reactions and bimolecular reactions over potential wells. The section on gas-phase state-selected reactions focuses on electronically adiabatic reactions and electronically nonadiabatic reactions. Finally, the section on condensed-phase bimolecular reactions covers reactions in liquids, reactions on surfaces and in solids and tunneling at low temperature.

Modeling the Kinetics of Bimolecular Reactions

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.

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Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications.

Quantum chemistry studies of ethylene carbonate (EC) and dimethyl carbonate (DMC) complexes with Li+ and LiPF6 have been conducted. We found that Li+ complexation significantly stabilizes the highly polar cis−trans DMC conformation relative to the nearly nonpolar gas-phase low energy cis−cis conformer. As a consequence, the binding of Li+ to EC in the gas phase is not as favorable relative to binding to DMC as previously reported. Furthermore, quantum chemistry studies reveal that, when complexation of LiPF6 ion pairs is considered, the DMC/LiPF6 complex is about 1 kcal/mol more stable than the EC/LiPF6 complex. The EC3DMC(cis−cis)/Li+ complex was found to be the most energetically stable among ECnDMCm/Li+ (n + m = 4) investigated complexes followed by EC4/Li+. Results of the quantum chemistry studies of these complexes were utilized in the development of a many-body polarizable force field for EC:DMC/LiPF6 electrolytes. Molecular dynamics (MD) simulations of EC/LiPF6, DMC/LiPF6, and mixed solvent EC:DMC/...

Quantum chemistry and molecular dynamics simulation study of dimethyl carbonate: ethylene carbonate electrolytes doped with LiPF6.

Plastic-bonded explosives are heterogeneous materials. Improved burn models for weak initiation relevant to accident scenarios require a better understanding of the physics associated with the formation and growth of hot spots. Since the relevant length scale is subgrain in extent, mesoscale simulations are needed to study hot spots. Mesoscale simulations require as input constitutive properties of an explosive grain. In addition, it is essential to account for physical dissipative mechanisms since hot spots represent local peaks in the fluctuations of the temperature field. Here, constitutive properties of the explosive HMX needed for mesoscale simulations are discussed and experimental data reviewed. Because some decomposition may occur during a measurement, it is difficult to account for systematic error in the data. To get a sense of the uncertainties in material parameters, it is necessary to examine all the available data. In addition, we discuss results from molecular dynamics simulations of some p...

Constituent properties of HMX needed for mesoscale simulations

Atomistic simulations were used to calculate the isothermal elastic properties for β-, α-, and δ-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). The room-temperature isotherm for each polymorph was computed in the pressure interval 0⩽p⩽10.6 GPa and was used to extract the initial isothermal bulk modulus Ko and its pressure derivative using equations of state employed previously in experimental studies of the β-HMX isotherm. The complete elastic tensor for each polymorph was calculated at room temperature and atmospheric pressure. For the case of β-HMX, the calculated elastic tensor is compared to one based on a fit to sound speed data yielding reasonably good agreement. The bulk modulus of β-HMX obtained from equation-of-state fits to the room-temperature isotherm agrees well with that determined from the complete elastic tensor and from volume fluctuations at atmospheric pressure. However, the value of Ko obtained from the isotherm is sensitive to choice of equation of state fitting form and to the weighting scheme employed in the fit. Based upon simulation results and reanalysis of experimental data, the commonly accepted value of the initial isothermal bulk modulus for β-HMX should be revised from a value of ∼12.4–13.5 GPa to ∼15–16 GPa. The present report provides the first accurate determination of the elastic tensors and isotropic moduli for α- and δ-HMX. Predicted values of the shear moduli for α- and δ-HMX are more than a factor of 2 smaller than for β-HMX.

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A molecular dynamics simulation study of elastic properties of HMX

We examine methods for dealing with the flow of zero‐point energy in classical trajectory simulations and identify some of the problems associated with their use. Fundamental issues which must be considered, both in assessing the extent of the zero‐point energy problem and in the development of useful remedies, are discussed.

Analysis of the zero‐point energy problem in classical trajectory simulations

Molecular dynamics simulations using a recently developed quantum chemistry-based atomistic force field [J. Phys. Chem. B, 103 (1999) 3570 ] were performed in order to obtain unit cell parameters, coefficients of thermal expansion, and heats of sublimation for the three pure crystal polymorphs of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). The predictions for β-, α-, and δ-HMX showed good agreement with the available experimental data. For the case of β-HMX, anisotropic sound speeds were calculated from the molecular dynamics simulation-predicted elastic coefficients and compared with recent Impulsive Stimulated Light Scattering (ISLS) sound speed measurements. The level of agreement is encouraging.

Molecular dynamics simulations of HMX crystal polymorphs using a flexible molecule force field

We have devised a semiclassical procedure based on the Makri–Miller [J. Chem. Phys. 91, 4026 (1989)] model for calculating the eigenvalue splitting in many‐atom systems and have used it to calculate the ground‐state splitting in several isotopomers of malonaldehyde. A potential‐energy surface that includes all twenty‐one vibrational degrees of freedom was constructed based on the available theoretical and experimental information. The results for calculations in which all atoms are allowed full three‐dimensional motion are in good agreement with the experimentally measured values. Restricting the molecular motion to a plane leads to an increase in the splitting due to a decrease in the average height and width of the barrier to tunneling when the molecule is not allowed to vibrate transverse to the molecular plane. Low energy mode‐specific excitations were used to study the sensitivity of the splitting to the motions of heavy atoms. The results show that the heavy atom motions have significant influence o...

Thomas D. Sewell

Papers

Constituent properties of HMX needed for mesoscale simulations

A molecular dynamics simulation study of elastic properties of HMX

Analysis of the zero‐point energy problem in classical trajectory simulations

Molecular dynamics simulations of HMX crystal polymorphs using a flexible molecule force field

Semiclassical calculations of tunneling splitting in malonaldehyde