Computer simulations of molecular dynamics

Gunsteren W F and H J C Berendsen 1990. Computer Simulation of Molecular Dynamics Methodology, Applications and Perspectives in Chemistry. Angewandte Chemie International Edition in English 29 992-1023. 

See van Gunsteren, W.F. Berendsen, H.J.C. Computer simulation of molecular dynamics-methodology, applications, and perspectives in chemistry Angewandre Chemie, International Edition in English, 29 992-1023, 1990, and Karplus, M. Petsko, G.A. Molecular dynamics simulations in biology Nature 347 631-639, 1990. 

In the case of molten salts, no obvious model based on statistical mechanics is available because the absence of solvent results in very strong pair correlation effects. It will be shown that the fundamental properties of these liquids can be described by quasi-chemical models or, alternatively, by computer simulation of molecular dynamics (MD). 

None of the methods currently used to study molecular dynamics can span the whole time range of motions of interest, from picoseconds to seconds and minutes. However, the structural resolution of a method is of equal importance. A method has to not only provide information about the existence of motions with definite velocities but also to identify what structural element is moving and what is the mechanism of motion. Computer simulation of molecular dynamics has proved to be a very important tool for the development of theories concerning times and mechanisms of motions in proteins. In this approach, the initial coordinates and forces on each atom are input into the calculations, and classical equations of motions are solved by numerical means. The lengthy duration of the calculation procedure, even with powerful modem computers, does not permit the time interval investigated to be extended beyond hundreds of picoseconds. In addition, there are strong... 

Van Gunsteren WF Berendsen HJC. Computer simulation of molecular dynamics methodology, application and perspectives in chemistry. Angew. Chem. Int. Ed. Eng. 1990 29 992-996. 

Such a time scale separation between system and bath may often be appropriate when dealing with intramolecular vibrational motions of molecules but is likely never appropriate for electronic transitions in solution near room temperature. In the past 10 years much effort has been devoted to dynamical aspects of the solvation process in polar liquids utilizing experiments [2-4], theory [5, 6], and computer simulations of molecular dynamics [7-10]. The... 

The only evidence for this partial dielectric saturation of polar solvents in the field of ions is the results of some computer simulations of molecular dynamics, following the Monte-Carlo method [87], It is claimed that these show dielectric saturation up to a distance of about 1 A from the solute s molecular envelope. Such a thin shell does not accommodate a single solvent molecule and for this reason the dielectric saturation is called partial. 

Computer Simulation of Molecular Dynamics Methodology, Applications, and Perspectives in Chemistry. 

Experimental determination of excess molar quantities such as excess molar enthalpy and excess molar volume is very important for the discussion of solution properties of binary liquids. Recently, calculation of these thermodynamic quantities becomes possible by computer simulation of molecular dynamics (MD) and Monte Carlo (MC) methods. On the other hand, the integral equation theory has played an essential role in the statistical thermodynamics of solution. The simulation and the integral equation theory may be complementary but the integral equation theory has the great advantage over simulation that it is computationally easier to handle and it permits us to estimate the differential thermodynamic quantities. 

In Part II we are concerned with CILS of liquids and solids. Computer simulation of molecular dynamics has emerged as a most powerful technique for the study of simple liquids and solids, and we include here such work as far as it is related to CILS because molecular dynamics studies are usually aimed at simulating the dense phases. This part is divided into three sections the first one considers the general theory of light scattering in the dense states related to CILS, the internal field problem, and so on. Section 2 is concerned with the CILS spectra of liquids, mostly, of course, of ordinary liquids and solutions, but work concerning superfluids and ionic melts is also included. Section 3 deals with the CILS-related spectra of amorphous and crystalline solids that have been prominently featured in the recent 22nd Faraday Symposium [435]. 

Computer simulation of molecular dynamics is concerned with solving numerically the simultaneous equations of motion for a few hundred atoms or molecules that interact via specified potentials. One thus obtains the coordinates and velocities of the ensemble as a function of time that describe the structure and correlations of the sample. If a model of the induced polarizabilities is adopted, the spectral lineshapes can be obtained, often with certain quantum corrections [425,426]. One primary concern is, of course, to account as accurately as possible for the pairwise interactions so that by carefully comparing the calculated with the measured band shapes, new information concerning the effects of irreducible contributions of inter-molecular potential and cluster polarizabilities can be identified eventually. Pioneering work has pointed out significant effects of irreducible long-range forces of the Axilrod-Teller triple-dipole type [10]. Very recently, on the basis of combined computer simulation and experimental CILS studies, claims have been made that irreducible three-body contributions are observable, for example, in dense krypton [221]. 

W. F. van Gunsteren and H. J. C. Berendsen, Angew. Chem., Int. Ed. Engl., 29,992 (1990). Computer Simulation of Molecular Dynamics—Methodology, Applications and Perspectives, in Chemistry. 

Volume 6 begins with two chapters on the computer simulation of molecular dynamics in fluids. The first of these chapters is concerned with fluids consisting of hard elastic particles, whereas the second of these chapters is concerned with particles that interact via a continuous pair potential. These techniques have led to a renaissance in the theory of fluids by providing an accurate picture of fluids with known force laws. The chapters on molecular dynamics are followed by two chapters on the kinetic theory of fluids. The first of the chapters covers many new topics in the kinetic theory of gases including the role of correlated collisions in producing long time-persistent effects and... 

In the vicinity of biomolecules, water may adopt very different behavior depending on the nature of the sites, on the available free volume, on temperature, etc. Due to the difficulty of experiments that can identify local properties among a variety of possibilities, the number of unambiguous results remains scarce. It is plausible that the development of computer simulations of molecular dynamics will soon take into account more precisely local environments [39-41]. 

The basis of our approach is the notion of local equilibrium. For a very large class of systems that are not in thermodynamic equilibrium, thermodynamic quantities such as temperature, concentration, pressure and internal energy remain well-defined concepts locally, i.e. one could meaningfully formulate a thermodynamic description of a system in which intensive variables such as temperature and pressure are" well defined in each elemental volume, and extensive variables such as entropy and internal energy are replaced by their corresponding densities. Thus, thermodynamic variables can be considered as functions of position and time. This is the assumption of local equilibrium. There are systems in which this assumption is not a good approximation but they are exceptional. In most hydrodynamic and chemical systems, local equilibrium is an excellent approximation. Modem computer simulations of molecular dynamics have shown that if initially the system is in such a state that... 

The temperature is identified through relation (15.1.4), in which m is the mass of the molecule and is the Boltzmann constant. In practice, only under very extreme conditions do we find significant deviations from the Maxwell distribution. Any initial distribution of velocities quickly becomes Maxwellian due to molecular collisions. Computer simulations of molecular dynamics have revealed that the Maxwell distribution is reached in less than 10 times the average time between collisions, which in a gas at a pressure of 1 atm is about 10 s [1]. Consequently, physical processes that perturb the system significantly from the Maxwell distribution have to be very rapid. A detailed statistical mechanical analysis of the assumption of local equilibrium can be found in [2]. 

---