Molecular Dynamics Simulation Program Research Articles

Expressions for forces and torques in molecular simulations using rigid bodies

Expressions for intermolecular forces and torques, derived from pair potentials between rigid non-spherical units, are presented. The aim is to give compact and clear expressions, which are easily generalized, and which minimize the risk of error in writing molecular dynamics simulation programs. It is anticipated that these expressions will be useful in the simulation of liquid crystalline systems, and in coarse-grained modelling of macromolecules.

Beam–plasma interaction in strongly coupled plasmas

The well-known problem of beam–plasma instability acquires new aspects when one or both of the two components (the beam and the plasma) are strongly interacting. We have now theoretically considered the case when the plasma is in the solid phase and forms a lattice. In this situation, the inherent anisotropy of the lattice leads to a coupling between the longitudinal and transverse polarizations. One of the novel features of the beam–plasma instability in this scenario is the possible excitation of transverse modes, which should be an experimentally observable signature of the instability. We have initially concentrated on a 2D toy model with the beam lying in the lattice plane. At the same time, we have initiated a molecular dynamics simulation program for studying various aspects of the penetration of a beam into a plasma lattice. The beam parameters can be adjusted in order to see the effects of increasing coupling strength within the beam and to distinguish between collective phenomena and scattering on individual particles. When both components are strongly interacting, a number of remarkable phenomena—trapping of beam particles, creation of dislocations, local melting of the lattice—may be observed.

A general purpose parallel molecular dynamics simulation program

We present a general purpose parallel molecular dynamics simulation code. The code can handle NVE, NVT, and NPT ensemble molecular dynamics, Langevin dynamics, and dissipative particle dynamics. Long-range interactions are handled by using the smooth particle mesh Ewald method. The implicit solvent model using solvent-accessible surface area was also implemented. Benchmark results using molecular dynamics, Langevin dynamics, and dissipative particle dynamics are given. Program summary Title of program:MM_PAR Catalogue identifier:ADXP_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADXP_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which it has been tested:any UNIX machine. The code has been tested on Linux cluster and IBM p690 Operating systems or monitors under which the program has been tested:Linux, AIX Programming language used:C Memory required to execute with typical data:∼60 MB for a system of ∼ 24 000 atoms Has the code been vectorized or parallelized? parallelized with MPI using atom decomposition and domain decomposition No. of lines in distributed program, including test data, etc.:171 427 No. of bytes in distributed program, including test data, etc.:4 558 773 Distribution format:tar.gz External routines/libraries used:FFTW free software ( http://www.fftw.org) Nature of physical problem:Structural, thermodynamic, and dynamical properties of fluids and solids from microscopic scales to mesoscopic scales. Method of solution:Molecular dynamics simulation in NVE, NVT, and NPT ensemble, Langevin dynamics simulation, dissipative particle dynamics simulation. Typical running time:Table below shows the typical run times for the four test programs. Benchmark results. The values in the parenthesis are the number of processors used System Method Timing for 100 steps in seconds 256 TIP3P MD 23.8 (1) 64 DMPC + 1645 TIP3P MD 890 (1) 528 (2) 326 (4) 209 (8) 8 A β 16 – 22 LD 1.02 (1) 23760 Groot–Warren particles DPD 22.16 (1)

A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical–molecular-mechanical calculations

We describe a regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical (QM)-molecular-mechanical (MM) calculations. To remedy the nonphysical QM/MM Coulomb interaction at short distances arising from a point electrostatic potential (ESP) charge of the MM atom and also to accommodate the effect of polarized MM atom in the coupling Hamiltonian, we propose a partial-wave expansion of the ESP charge and describe the effect of a s-wave expansion, extended over the covalent radius r(c), of the MM atom. The resulting potential describes that, at short distances, large scale cancellation of Coulomb interaction arises intrinsically from the localized expansion of the MM point charge and the potential self-consistently reduces to 1r(c) at zero distance providing a renormalization to the Coulomb energy near interatomic separations. Employing this renormalized Hamiltonian, we developed an interface between the Car-Parrinello molecular-dynamics program and the classical molecular-dynamics simulation program Groningen machine for chemical simulations. With this hybrid code we performed QM/MM calculations on water dimer, imidazole carbon monoxide (CO) complex, and imidazole-heme-CO complex with CO interacting with another imidazole. The QM/MM results are in excellent agreement with experimental data for the geometry of these complexes and other computational data found in literature.

PARALLELIZATION OF A MOLECULAR DYNAMICS SIMULATION OF AN ION-SURFACE COLLISION SYSTEM: Ar–Ni(100)

Parallel molecular dynamics simulation study of the ion-surface collision system is reported. A sequential molecular dynamics simulation program is converted into a parallel code utilizing the concept of parallel virtual machine (PVM). An effective and favorable algorithm is developed. Our parallelization of the algorithm shows that it is more efficient because of the optimal pair listing, linear scaling, and constant behavior of the internode communications. The code is tested in a distributed memory system consisting of a cluster of eight PCs that run under Linux (Debian 2.4.20 kernel). Our results on the collision system are discussed based on the speed up, efficiency and the system size. Furthermore, the code is used for a full simulation of the Ar–Ni (100) collision system and calculated physical quantities are presented.

OOPSE: An object‐oriented parallel simulation engine for molecular dynamics

OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.

Large scale MD simulation of 8-oxoguanine and AP site multiple lesioned DNA molecule combined with biomolecular visualization software

The visualization of a real picture and dynamical movements of biomolecules is an essential process for understanding their fundamental properties, although there are few systems that can be used in combination with existing dynamical computer codes. Presented here is the novel system, Fujitsu Bio Molecular Visualization System (F-BMVS), which enables to produce real pictures and an animation by arranging them along a time series of a large-scale simulation of biomolecules associated with a molecular dynamics (MD) simulation program. This animation system is used to study the results of MD code, AMBER, in order to find structural differences on the lesioned DNA comparing with non-damaged DNA. Compared with non-damaged DNA molecule, it was found that the lesioned one has two specific features—bending at the lesioned site and flipping out apurinic/apyrimidinic site. These results are supported by the dynamical analysis of structural properties of DNA molecules. Product of visualization also suggests that presented animation system has a great advantage for understanding certain properties of biomolecules in a dynamical mode.

Interaction energy surfaces of small hydrocarbon molecules

Nonbonding interactions of small alkane molecules were studied with ab initio methods. Previously reported energy data for ethane and propane dimers were supplemented with 1747 new configurations of dimers involving slightly larger hydrocarbons. The completed work provides interaction energy surfaces for all combinations of dimer pairs involving ethane, propane, isobutane, and neopentane and thus contains information of all chemical groups found in acyclic alkanes. The strongest attraction of the studied molecule pairs was encountered in isobutane C2h dimer, where an energy minimum of −1.784 kcal mol−1 at 4.28 Å separation of centermost carbon atoms was observed. The composite data set was fitted with a modified Morse pair potential energy function representing each interatomic C–C, C–H, and H–H interaction for easy transfer to molecular dynamics simulation programs. The new generic parameter set was shown to describe the ab initio data for these small alkane molecules with good accuracy. Qualitative comparisons with previously reported potential models were also made, and the relative capability of the models to reproduce quantum-chemical potential energy surfaces was investigated.

DEFECT CREATION CHANNEL MEDIATED BY HOLE EXCITATION IN KBR: A MOLECULAR DYNAMICS STUDY

There have been suggestions that the radiation defect pair (F-H centers) in alkali halide crystals can be generated from higher excited states of exciton. Recent experimental works indicate production of fast F center before the self-trapped exciton (STE) is formed. In this paper the relaxation of an exciton in KBr crystal while the hole is in an excited state is presented. The study is based on a recently developed molecular dynamics (MD) simulation program. A cluster of about 150 atoms, containing a Frenkel-type free exciton embedded in an infinite lattice, is allowed to relax at 10 K. The hole is kept at low-lying excited states (of molecular orbitals g and u ) while the electron is localized at an anion site. The principal results are as follows: (1) Generally, the hole jumps about over the Br ions until it forms a molecule bond Br 2 when the excess kinetic energy (converted from the electronic excitation energy) has suitably dissipated. (2) Depending on the rate of energy dissipation, the molecule-type excited hole center appears as early as after 0.5 pico-second away from the F center. (3) The formed hole center, however, is a V k -center occupying two anion sites and is not a H-center occupying one anion site. These results are discussed with the recent observation of early F center creation.

Development and application of nonequilibrium simulation program for ion diffusion in battery

The regular molecular dynamics method cannot simulate the ion concentration gradient system because the number of particles in the system is constant during the simulation. In the present study, in order to overcome the above problem, we developed a new nonequilibrium molecular dynamics simulation program, which can be applied to the concentration gradient system, such as the ion diffusion in the solid state ionics materials. Moreover, we applied our new program to the LiCoO 2 system that has been used as a cathode material of the lithium battery. The new program succeeded to reproduce the lithium ion diffusion process from the higher concentration area to the lower concentration area and, hence, we confirmed the high ability of our new program to the simulation of the ion concentration gradient system.

Moldy: a portable molecular dynamics simulation program for serial and parallel computers

Moldy is a highly portable C program for performing molecular-dynamics simulations of solids and liquids using periodic boundary conditions. It runs in serial mode on a conventional workstation or on a parallel system using an interface to a parallel communications library such as MPI or BSP. The “replicated data” parallelization strategy is used to achieve reasonable performance with a minimal difference between serial and parallel code. The code has been optimized for high performance in both serial and parallel cases. The model system is completely specified in a run-time input file and may contain atoms, molecules or ions in any mixture. Molecules or molecular ions are treated in the rigid-molecule approximation and their rotational motion is modeled using quaternion methods. The equations of motion are integrated using a modified form of the Beeman algorithm. Simulations may be performed in the usual NVE ensemble or in isobaric and/or isothermal ensembles. Potential functions of the Lennard–Jones, 6-exp and MCY forms are supported and the code is structured to give an straightforward interface to add a new functional form. The Ewald method is used to calculate long-ranged electrostatic forces.

A MOLECULAR DYNAMICS RUN WITH 5 180 116 000 PARTICLES

We report on the development of IMD, a scalable program for classical molecular dynamics simulations on massively parallel supercomputers. New features like online-visualization and metacomputing are described.

Falcon: On‐line monitoring for steering parallel programs

Advances in high performance computing, communications and user interfaces enable developers to construct increasingly interactive high performance applications. The Falcon system presented in this paper supports such interactivity by providing runtime libraries, tools and user interfaces that permit the on-line monitoring and steering of large-scale parallel codes. The principal aspects of Falcon described in this paper are its abstractions and tools for capture and analysis of application-specific program information, performed on-line, with controlled latencies and scalable to parallel machines of substantial size. In addition, Falcon provides support for the on-line graphical display of monitoring information, and it allows programs to be steered during their execution, by human users or algorithmically. This paper presents our basic research motivation, outlines the Falcon system's functionality, and includes a detailed evaluation of its performance characteristics in light of its principal contributions. Falcon's functionality and performance evaluation are driven by our experiences with large-scale parallel applications being developed with end users in physics and in atmospheric sciences. The sample application highlighted in this paper is a molecular dynamics simulation program (MD) used by physicists to study the statistical mechanics of liquids. © 1998 John Wiley & Sons, Ltd.

Falcon: On-line monitoring for steering parallel programs

Advances in high performance computing, communications and user interfaces enable developers to construct increasingly interactive high performance applications. The Falcon system presented in this paper supports such interactivity by providing runtime libraries, tools and user interfaces that permit the on-line monitoring and steering of large-scale parallel codes. The principal aspects of Falcon described in this paper are its abstractions and tools for capture and analysis of application-specific program information, performed on-line, with controlled latencies and scalable to parallel machines of substantial size. In addition, Falcon provides support for the on-line graphical display of monitoring information, and it allows programs to be steered during their execution, by human users or algorithmically. This paper presents our basic research motivation, outlines the Falcon system's functionality, and includes a detailed evaluation of its performance characteristics in light of its principal contributions. Falcon's functionality and performance evaluation are driven by our experiences with large-scale parallel applications being developed with end users in physics and in atmospheric sciences. The sample application highlighted in this paper is a molecular dynamics simulation program (MD) used by physicists to study the statistical mechanics of liquids. © 1998 John Wiley & Sons, Ltd.

MOLDA for Windows-A Molecular Modeling and Molecular Graphics Program Using a VRML Viewer on Personal Computers.

MOLDA for Windows, an interactive personal-computer molecular modeling and molecular graphics program, which can be used as an interface to the ab initio molecular orbital program GAUSSIAN 94, the molecular dynamics simulation program AMBER 4.0 and the molecular mechanics program MM2, is described. The molecular model constructed by using MOLDA can be transferred to the Virtual Reality Modeling Language (VRML) format file and viewed by using a VRML viewer on the World Wide Web (WWW).

Parallel molecular dynamics on a multi signalprocessor system

This paper gives an overview of a parallel computer architecture called MUSIC (Multi Signalprocessor System with Intelligent Communication), which has been developed at the Swiss Federal Institute of Technology. The current version achieves a peak performance of 3.8 GFlops. We discuss the system software and tools used to program the system and then present our implementation of a molecular dynamics simulation program which uses the architecture of MUSIC in an efficient way. We demonstrate the correctness of our implementation and give measurements of the performance of the system. To the best of our knowledge, MUSIC outperforms the most powerful present-day vector supercomputers.

Comparison of the Performance of a Program for Molecular Dynamics Simulations of Liquids on Different Computers

Comparison of the Performance of a Program for Molecular Dynamics Simulations of Liquids on Different Computers

Evidence for heavy ion channeling in AlGaAs at low energies

We used a new molecular dynamics simulation program to model the scattering of low-energy ions into the relatively open 〈011〉 axial channels of zinc-blende crystals. We also implanted 1–5 keV Si ions into GaAs/AlGaAs multiple-quantum well samples and used secondary ion mass spectrometry and photoluminescence to search for the deep ion penetration and optical damage which are characteristic of this ion channeling. Both the simulated and measured Si depth distributions have exponential tails extending at least 20 times further than the mean ion range. The photoluminescence efficiencies are severely degraded in the quantum wells which are overlapped by the observed Si profile tails. These results suggest that unintentional ion channeling is a major factor in the extensive degradation of optical and electrical properties of semiconductor surfaces which are exposed to low-energy ion bombardment during device fabrication.

Efficiency in statistical mechanical simulations of biomolecules — computer programs for molecular and continuum modelling

A strategy for biomolecular simulations is described. It includes a molecular dynamics (MD) simulation program and a Monte Carlo (MC) simulation program. The former provides a molecular description including a classical treatment of covalent bonds and bond angles. The MD program has been carefully tuned for optimal efficiency, while remaining completely general and capable of handling all kinds of mixtures of flexible molecules. It also allows one to incorporate 2D NMR constraints for structural refinement. The MC program is designed for studies of long-range electrostatic interactions - the basic system is an arbitrarily shaped charged aggregate solvated in a salt solution. The approach is based on a dielectric continuum model and only electrostatic interactions are treated explicitly. The solvent enters as a dielectric medium screening the electrostatic interactions with a appropriate dielectric permittivity.

Molecular dynamics simulation program of order N for condensed-matter systems: II. MDSPNL: pyramid with neighbour list, short-range interactions

A program of order N for molecular dynamics simulation is presented. The program enables one to simulate efficiently very large condensed-matter systems involving short-range interactions (e.g. simple liquids with pairwise-additive forces). The program is optimized for serial computers and on the Cyber 962-11 it attains a speed of more than 5000 particles/cpu s.